Extended Data Fig. 3: DCC lineage cells expand in response to C.r infection and respond to microbes and localized T cells.

scRNA-seq was performed on epithelial cells from mid-distal colon of naïve BL/6 mice. a, Heatmap of top genes from combined naïve and infected BL/6 mice defining each major IEC subset. b, scVelocity plots show transcriptional relationships between the major IEC subsets. Arrowheads denote directionality and lines represent kinetics of differentiation. 2 mice pooled per sample, n = 2 biological replicates per group. Wilcoxon rank sum test, p-val<0.05 was used for differential gene expression analyses. See Supplementary Table 2 for top expressed genes per cluster. c-e, IECs from proximal colon (blue) and distal colon (red) of naïve BL/6 (white), GF (color) and Rag1^–/– (grey) mice were stained for Ly6G, Fabp2, EpCAM1, CD45 and L/D dye, and analyzed by flow cytometry (c) and enumerated per cm of tissue (d) or sorted on EpCAM1⁺CD45^–L/D dye^– IECs and mRNA expression analyzed by RT-PCR (e). 3-4 mice per group; n = 2 independent experiments. Two-way ANOVA; *p≤0.05, **p≤0.01 and ***p≤0.001. IEC=intestinal epithelial cell; PCC=proximal colonocyte; DCC=distal colonocyte; DCS=deep crypt secretory cell; TA=transit-amplifying cell; CBC=crypt base columnar cell; Abs= absorptive; Sec=secretory; Undiff=undifferentiated; Prog=progenitor; ns=not significant.