FRC in human ileal GALT include spatially distinct subclusters. (A) UMAP representation of pooled ileal GALT FRC showing the six subclusters. (B) UMAP representations of GALT FRC only from PP (left plot) and M-ILF (right plot). (C) Violin plots showing the expression levels of the FRC markers CD24 and CLU by the indicated ileal GALT FRC subclusters of PP (upper panels) and M-ILF (lower panels). (D) Heatmaps showing the scaled expression of the top ten DEG (left panel) and other canonical FRC markers (right panel) by the indicated subclusters. (A–D) Data based on 4,359 single cells from five (PP, 2,997 cells) and three (M-ILF, 1,362 cells) independently processed donors. (E) Confocal laser microscopy images of ileal GALT highlighting the 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. CXCL9⁺CXCL10⁺ FRC are abbreviated as CXCL10⁺ FRC in this and subsequent figures.