Fig. 2: Despite similar FB subset composition, small intestinal and colonic FB display regional transcriptional specialization.

a Heatmaps showing transcription levels (integrated data) of selected epithelial support genes by indicated MSC subsets. b Pearson correlations between averaged cluster expressions of Louvain clusters from scRNA-seq and bulk RNA-seq datasets based on 1937 (small intestine, left) and 1925 (colon, right) overlapping variable genes. Bulk RNA-seq data are from sorted MSC subsets from 3 independent experiments. Unsupervised hierarchical clustering indicates similarities of bulk RNA-seq subsets within each tissue. c, d Flow cytometric analysis of adult small intestinal (c) and colonic (d) Itgβ1⁺ MSCs from Ackr4.GFP mice. Representative staining from 2 experiments with 2–4 mice/experiment. Colored gates represent indicated MSC subsets. PCs pericytes, SMCs smooth muscle cells, FB fibroblast. e Principal component analysis (PCA) of bulk RNA-seq data from indicated sorted FB populations. Results are from 3 independent sorts/population. f Volcano plots showing differentially expressed genes (DEGs) between small intestinal and colonic PDGFRα^hi FB (left) and Fgfr2⁺ FB (right). Dotted horizontal line denotes significant adjusted p value (Benjamini–Hochberg correction) of 0.05, vertical dotted lines denote log₂FC = 0 and the log₂FC of ±1.5. g–j Heatmap representations of averaged transcription levels of indicated genes within sorted FB subsets. Data are averaged from 3 independent bulk RNA-seq datasets. g Epithelial support genes, h cytokines and cytokine receptors, i chemokines, j vitamin A metabolism. Gene lists for i were selected based on the epithelial support list in (a) while those in h–j were differentially expressed between either small intestinal and colonic PDGFRα^hi FB or between small intestinal and colonic Fgfr2⁺ FB. Identified DEG that are 1.5 < |log₂FC| are listed to the right of (g) or below (h–j) the heatmaps and. See also Supplementary Fig. 2.