FIG 3.

Global ISG expression in response to IFN-β is suppressed in vivo. IEC organoids or neonatal mice were treated for 4 h with PBS or IFN as described in the legends of Fig. 1 and 2, and isolated IECs were analyzed by RNA-seq. (A) Normalized read counts for Usp18. (B) PCA of the top 500 differentially expressed genes. (C to E) Venn diagrams showing the overlap in genes stimulated by the indicated IFN treatments relative to their matched PBS-treated controls. (F) Heat map comparing log₂-fold changes of 527 ISGs among organoid and neonate IFN treatment groups relative to matched PBS controls. (G and H) Log₂ normalized counts of the indicated IFN receptor genes (G) and heat map of IFN regulatory genes (H) from PBS-treated neonate and organoid IECs. Differentially expressed genes (DEGs) listed in panel H are significantly different between neonate and organoid IECs (see Data Set S1 in the supplemental material). (I) Flow cytometry staining of IFNAR1 and IFNAR2 on neonate IECs (from Fig. 1E) and organoid IECs. Gray histograms are control stains (no IFNAR antibody), and bar graphs show geometric mean fluorescence intensities (MFI) of IFNAR fluorescence normalized to the controls. Data points represent results from replicate treatments (A, B, and G) or replicate experiments (I). Significance was determined by a t test (I). *, P < 0.05; **, P < 0.01.