Fig 1: While LP CD103+CD11b+ cDC2s express proinflammatory markers, intraepithelial cDC2s display an anti-inflammatory phenotype(A) Heatmap of scaled expression (log normalized UMI counts) of the top 20 most differentially expressed genes for each cluster. Antimicrobial genes are highlighted in orange, migration genes in red, inflammatory genes in blue, and cyclin genes in green.(B) Violin plots showing the expression of inflammatory genes: Il1b and Rel proto-oncogene (NF-?B subunit).(C) Violin plots showing the expression of Ccr7, CD83, and CD209a among clusters.(D) Left panel: plot of percentage of GFP positive cells in CD103+CD11b+ cDC2s as reporter of CCR7 expression in Ccr7gfp mice lamina propria and epithelium. Data are pooled from 4 independent experiments with n = 3–4 mice per experiment. Mean ± SEM, data were compared using mixed-effects analysis and Sidak’s multiple comparisons test, ****p < 0.0001. Right panel: geometric mean fluorescence intensity of CD83 comparing the expression in LP versus epithelial CD103+CD11b+ DCs. Mean ± SEM, data are pooled from 3 independent experiments with n = 2–3 mice per experiment.(E) Geometric mean fluorescence intensity of TNFa and IL-1ß measured by flow cytometry intracellular cytokine staining. Data are pooled from 3 independent experiments with n = 2–3 mice per experiment. For IL-1ß, data were normalized by experiment. Data were compared using t test.(F) Geometric mean fluorescence intensity of the costimulatory molecules CD86 and CD80 comparing the expression in CD103+CD11b+ DCs from epithelium and lamina propria. Data are pooled from 3 independent experiments, with n = 2–3 mice per experiment and were compared using Mann-Whitney test or t test.(G) Left panel: geometric mean fluorescence intensity of CD209a comparing the expression in LP versus epithelial CD103+CD11b+ DCs. Data are pooled from 3 independent experiments normalized by experiment with n = 2–3 mice per experiment and compared using t test. Right panel: Defa24 gene expression measured by quantitative real-time PCR. Fold change of epithelial over LP CD103+CD11b+ DCs expression normalized against the housekeeping Hprt. Data correspond to 3 independent experiments, with RNA obtained after pooling 4 mice per experiment. In (E)-(G), mean ± SEM, **p < 0.01, *** p < 0.001, **** p < 0.0001.