Extended Data Fig. 5: Identification and characterization of spatial niches in the small and large intestine.
From: Spatially restricted immune and microbiota-driven adaptation of the gut
a-c, Clustering of SI Visium data (resolution=0.2). (a) UMAPs showing the clustering. (b) Boxplots showing the fraction of each cluster. Box limits are the upper and lower quartiles; and whiskers are 1.5 times the interquartile range from the box (3 biological replicates per box). (c) Expression of marker genes for each cluster. d-e, Clustering of colon Visium data (resolution=0.8). (d) UMAPs showing the clustering. (e) Expression of marker genes for each cluster. f, Spatial distribution of each cluster on one example of SPF colon. g, Top 10 Gene Ontology (GO) terms (Biological Processes) enriched for marker genes of each colon section (top 500 maker genes ranked by Wilcoxon test p-value; all of them have adjusted p-value < 0.05; enriched GOs are significant with adjusted p-value < 0.05 by Fisher’s exact test). h, Spatial expression of middle colon enriched, microbiota induced genes Retnlb, Ang4, Itln1, Pnliprp2, and Pla2g4c on SPF colon tissue from 3 mice (top down). D, duodenum; J1, jejunum 1; J2, jejunum 2; I, ileum.
