(A) Schematics of the study to determine effects of TBI, IFN-γ, and ruxolitinib on intestinal epithelium in mice. Ileum tissue was collected 48 hours after TBI and analyzed. (B) Representative small intestines of control (C), IFN-γ (I), IFN-γ + ruxolitinib (IR), TBI (T), TBI + IFN-γ (TI), and TBI + IFN-γ + ruxolitinib (TIR) mice are shown. Scale bars: 8 cm. (C) Lengths of small bowels in cohort. Measurements from 2 experiments were combined and presented as mean ± SD; control group, n = 4; TIR, n = 7; remaining groups, n = 6. (D–G) Quantification of crypt numbers per ileum circumference section at 48 hours after TBI. Whole (D), cryptdin-1+ (E), Lgr5-GFP+ (F), and Olfm4+ (G) crypts were counted in 2 ileum circumference sections of 3 different Lgr5-EGFP-ires-creERT2 mice from each group. Data are from 2 separate experiments and show mean ± SD. (H and I) qRT-PCR analyses were performed to quantify mRNAs coding for lineage-specific markers, niche factors, and requisite lineage-determining transcription factors in whole terminal ileum tissue. Data from 2 separate experiments were combined and are shown as mean ± SEM; TIR group, n = 7; all other groups, n = 6 biological replicates. Tukey’s multiple comparisons test was used to compare each cohort. Mean values of data in C–G and statistical results in C–I are presented in Supplemental Tables 2–4.