FRC landscape of large intestinal SM-ILF. (A) Volcano plot showing DEG between GALT FRC from large intestinal SM-ILF and ileal GALT based on data from five independently processed donors (5× PP and SM-ILF, 3× M-ILF). (B) UMAP representation of large intestinal SM-ILF GALT FRC showing five subclusters. (C) Violin plots showing expression of the FRC markers CD24 and CLU by the indicated SM-ILF FRC subclusters. (D) Heatmaps showing the scaled expression of the top 10 DEG (left panel) and other canonical FB markers (right panel) by the indicated SM-ILF GALT FRC subclusters. (B–D) Data based on 14,786 single cells from five independently processed donors. (E) Confocal laser microscopy images of large intestinal SM-ILF showing expression of the indicated stromal and immune cell markers either at the protein (PDPN, CCL21, CD31, ColVI, CD3, CR1/2, CXCL13, CD19) or at the RNA (CCL19, CXCL14, CXCL10) level. The cyan star marks the apical side of the epithelial layer facing the intestinal lumen; the yellow star marks the follicle center. Images are representative of three replicates derived from different patients that were stained in two or three independent experiments. (F) Cluster identity key linking numerical FRC clusters with FRC subcluster designations in large intestinal (large int.) SM-ILF and ileal GALT. (G) Pearson correlation plots showing the overlap of FB subcluster signatures between ileal and large intestinal GALT FRC, based on all variable genes per cluster. Data are scaled within the same row, with the mean expression level of a signature score across all clusters in a row being set to zero.