Extended Data Fig. 3: Extended analysis of gLN stromal and dendritic cell differences according to gut segment drained.

a, Flow cytometry plot showing gating of FRCs and LECs for RNA-seq. Pre-gates indicated above. b–g, Some differentially regulated pathways among LECs sorted from duodenal versus colonic gLNs (NES, normalized enrichment scores) (b); differentially expressed genes among LECs sorted from ileal versus colonic gLNs or ileal versus duodenal gLNs (c, d); some differentially regulated pathways among FRCs sorted from duodenal versus colonic gLNs (e); differentially expressed genes among FRCs sorted from ileal versus colonic gLNs or ileal versus duodenal gLNs (f, g), all from SPF C57BL/6 mice and identified by RNA-seq. Blue, metabolism-related pathways or genes; red, immunity-related pathways or genes. h, Flow cytometry plot showing gating of CD103⁺CD11b⁺ and CD103⁺CD11b^– dendritic cells for RNA-seq. Pre-gates indicated above. i–l, Differentially expressed genes identified by RNA^-seq among CD103⁺CD11b⁺ (i, k) and CD103⁺CD11b^– (j, l) dendritic cells sorted from ileal versus colonic gLNs or ileal versus duodenal gLNs from SPF C57BL/6 mice. m, n, Some differentially regulated pathways among CD103⁺CD11b⁺ (m) and CD103⁺CD11b^– (n) dendritic cells sorted from duodenal versus colonic gLNs. o–q, Mean fluorescence intensity of fluorescein isothiocyanate-positive boron-dipyrromethene-tagged aminoacetate (Aldefluor) in CD103⁺CD11b^– (o), CD103⁺CD11b⁺ (p), and CD8α⁺ or CD11b⁺ (q) dendritic cells from gLNs from germ-free and SPF C57BL/6 mice (n = 3) assessed by flow cytometry 30 min after the addition of substrate. r, Ratio of CD103⁺CD11b⁺ to CD103⁺CD11b^– dendritic cells in gLNs from SPF and germ-free mice (n = 4, representative of two independent experiments⁾. *P < 0.05, **P < 0^.01, ***P < 0.005; ns, not significant (one-tailed t-test or ANOVA).