Fig. 3: Macrophage populations are enriched in the LP microniche.
a, Left, UMAP visualization of total myeloid subsets across all locations. Middle, UMAP of total myeloid populations by tissue microniche. Right, myeloid subset distribution (top) and total cell numbers at the indicated locations (bottom). b, log2-transformed fold difference of proportions of myeloid, T cells and ILCs in LA and LP. c, Representative CD11c and SIRPα immunofluorescence and DAPI staining in Hh-infected caecum tissue, showing an LA and surrounding LP. Scale bar, 50 μm. d, Representative CD206 immunofluorescence and DAPI staining in Hh-infected caecum tissue showing an LA and surrounding LP. Scale bars 50 μm. e, Densities of CD11c+SIRPα+ dendritic cells and CD206+ macrophages in the LA and LP microniches of Hh-infected caecum tissue. f, Violin plots of MHCII expression score across lymphoid and myeloid cells in the LP (top) and LA (bottom). Restricted to cell types with more than 30 cells per region. g, Relative mean expression of genes associated with STAT3 signalling and receptors in myeloid and lymphoid subsets in the LA and LP. Restricted to cell types with more than 30 cells per region. a,b,f,g, One sequencing run from four T cell compartments from six combined mice. c–e, Two independent experiments with n = 6 per group. Each dot represents data from one individual mouse. e, One-way ANOVA using Tukey’s multiple comparisons test.
