Generation, processing, and analysis of scRNA-seq FB datasets. (A) Representative flow cytometry plots showing the gating strategy for the identification and sorting of stromal cells, excluding dead cells, CD235ab⁺ red blood cells, EpCAM⁺ epithelial cells, CD45⁺ immune cells, and CD45^loCD19^+/−CD38^hi plasma cells. (B) UMAP representation of scRNA-seq results before removal of contaminating non-FB. (C) Identification of contaminating non-FB based on gene sets characteristic for the indicated cell types. (D) Identification of FB based on their expression of the indicated FB signature markers. Red circle marks FB. (E) Pie charts showing the abundance of FB clusters pooled by tissue and site of origin. (F) Bar plot showing the abundance of each FB cluster as a fraction of total FB in each sample by donor and tissue origin. (G) Identification of intestinal FB subsets according to Kinchen et al. (2018) on the combined dataset including all LP, SM, and GALT-derived cells based on an overlay of the top 10 DEG per cluster identified in the original Kinchen et al. (2018) publication. (B–G) Data include cells from five tissue donors (5× PP and SM-ILF, 3× M-ILF and LP, 1× SM). All available tissues from a given donor were processed together in a single experiment, and each donor was processed separately.