Extended Data Fig. 8: Single-cell coupled with spatial transcriptomics reveals spatially restricted structural cell subsets and spatially restricted adaptations to the microbiota.
From: Spatially restricted immune and microbiota-driven adaptation of the gut
a, Estimated abundance (Cell2location on Visium samples from 3 biological replicates; cells with abundance lower than 0.5 or one standard deviation from the mean for each cell type are removed) of spatially variable structural cell subsets (the center line is the median; box limits are the upper and lower quartiles; and whiskers are 1.5 times the interquartile range). b, Distribution of spatially variable structural cell subsets mapped onto space for colon tissue (Xenium). c-d, Spatial heatmaps showing the counts of cell types (Z-score) assigned to the Xenium sample of SPF mouse colon. The heatmap columns are arranged based on the coordinates of the unrolled proximal-distal axis from left to right (c; summarized into 1000 bins) and projected serosa-mucosa axis (d; summarized into 50 bins). e, Expression of marker genes for enterocytes. f, Antibody staining of SLC9A3 protein (green) on colon tissue. Nuclei are stained with DAPI (grey). Image is representative of n = 3 biological replicates. g, Expression of marker genes for fibroblasts. h, Expression of marker genes for goblet cells. i, UMAP of RNA velocity analysis of goblet cell subtypes.
