Fig. 2: Gene expression profiles in infected intestinal epithelium and cell cultures.

a Expression of IFNs in intestinal epithelium from infected Ifnar1^fl/fl neonates. Mice (5 days old) were orally inoculated with C. parvum (10⁶ oocysts/animal) and ileal epithelium (4 cm from the ileocecal junction) was isolated at 48 h p.i. IFN gene expression was evaluated by RT-qPCR and presented as fold change to uninfected control. Dots represent data from experiment with six mice in each group and presented as mean values ± SD. b Expression of IFNs in infected IEC4.1 cells. IFN gene expression (24 h p.i.) was evaluated by RT-qPCR. Ifn-β1 protein content in the supernatants (24 h and 48 h p.i.) was measured by ELISA. Data are from three biological replicates and presented as mean values ± SD. p values were determined by two-tailed unpaired Student’s t-test (in a and b). c Gene expression profiles in intestinal epithelium from infected neonates (48 h and 72 h p.i.) by RNA-Seq. The numbers of genes with an altered expression level following infection are listed. d Gene set enrichment analysis (GSEA) in intestinal epithelium from infected Ifnar1^fl/fl (48 h p.i.) compared with that in uninfected Ifnar1^fl/fl or infected Villin.Ifnar1^−/− neonates (48 h p.i.). p values were calculated based on Kolmogorov–Smirnov test and adjusted by Benjamini–Hochberg method. Normalized enrichment scores and adjusted p values for the signaling pathways are shown. e Selected gene groups revealed by RNA-Seq in intestinal epithelium from infected Ifnar1^fl/fl and Villin.Ifnar1^−/− neonates (48 h. p.i.). Representative genes for type I/II/III IFN signaling and misc. upregulated genes (expression levels further increased in infected Villin.Ifnar1^−/− neonates) are shown. f Volcano plots depicting the differentially upregulated genes between infected Villin.Ifnar1^−/− and Ifnar1^fl/fl animals (48 h p.i.). Two-tailed Wald tests were performed for statistical analysis and p value was adjusted by Benjamini–Hochberg method. Dashed line indicates a false discovery rate cutoff of 0.05. Data are from three animals for each group (c–f). g Gene expression profiles in IEC4.1 following infection. Numbers of genes whose expression levels were significantly altered in infected IEC4.1 and IEC4.1-Ifnar1^−/− cells (24 h p.i.) by RNA-Seq are listed. h GSEA of gene expression profiles in infected IEC4.1-Ifnar1^−/− cells (24 h p.i.) compared with that in infected IEC4.1 cells (24 h p.i.). Data are from three biological replicates (3 RNA-seq replicates each group) in g and h. p values (in h) were calculated based on Kolmogorov–Smirnov test and adjusted by Benjamini–Hochberg method. Normalized enrichment scores and adjusted p values for the signaling pathways are shown. Source data are provided as a Source Data file.