Extended Data Fig. 1: Experiential and computational construction of the transcriptional landscape of the intestine.
From: Spatially restricted immune and microbiota-driven adaptation of the gut
a, Hematoxylin and eosin (H&E) stain images of the partitioned intestine. b, Boxplots showing the number of genes detected in each spot on each Visium slide (the center line is the median; box limits are the upper and lower quartiles; and whiskers show 1.5 times the interquartile range from the box). The line on the secondary Y-axis shows the number of spots with tissue on each Visium slide. (For intestinal regions, data is shown for n = 3 SPF and GF mice and n = 2 FMT mice. For DSS and light/dark cycle, data from n = 1 SPF or GF mouse is shown). c, Schematic of experimental design (created using R, Adobe Illustrator and BioRender (credit: H. Kang, https://biorender.com/l58o103; 2024). d, Expression of Epcam (left) and Tagln (right) in each Visium spot on the unrolled and aligned axes. e, Clusters of Visium spots (Louvain algorithm with clustering resolution =0.5) shown on the original Visium slide (top) and the unrolled and aligned axes (bottom). f, Cluster annotation of spots along the serosa-epithelium axis (top). Dot plot (bottom) of marker genes for each annotated cluster (top 20 genes in each cluster ranked by Wilcoxon rank sum test p-values; all of them have adjusted p-value < 0.05; expressed in >50% within the cluster and <30% in other clusters). g, Module score for each cell type (Methods) in different tissue layers. D, duodenum; J1, jejunum 1; J2, jejunum 2; I, ileum; C, colon.
