Fig. 4: CD4⁺CD8αα⁺ IEL-related genes are abundant in Ccr9^−/− mice.

a Pseudotime analysis of sequenced IELs originating from Ccr9^+/+ mice (left) and Ccr9^−/− mice (right), color-coded by pseudotime gradient. Numbers on the UMAP figure indicate the cluster numbers. b Violin plots show expression of Runx3, Tbx21, and Cbfb among IELs from clusters 0, 4, and 7 (CD4⁺CD8αα⁺ T cells); clusters 1, 2 and 3 (CD4⁺CD8αα⁻ T cells); and clusters 10, 13 and 14 (CD4⁺CD8αα^int T cells). c Violin plots show the expression of Runx3, Tbx21, and Cbfb among IELs from clusters 0, 4, and 7 (CD4⁺CD8αα⁺ T cells); clusters 1, 2 and 3 (CD4⁺CD8αα⁻ T cells); and clusters 10, 13, and 14 (CD4⁺CD8αα^+int T cells) from Ccr9^+/+ and Ccr9^−/− mice (a–c; n = 3 biologically independent IEL samples for each strain). One-way ANOVA with Tukey’s multiple comparisons post-hoc test (b) or the two-sided Student’s t test (c) was applied. Source data are provided as a Source data file.