Fig. 3: Single-cell transcriptomic analysis of human palatine tonsil stromal cells. | Nature Immunology

Fig. 3: Single-cell transcriptomic analysis of human palatine tonsil stromal cells.

From: PI16+ reticular cells in human palatine tonsils govern T cell activity in distinct subepithelial niches

Fig. 3

a, Schematic representation of the scRNA-seq workflow. b, UMAP showing 14 CD45−CD235a− stromal cell clusters after removal of contaminating cells (Methods) including BECs, LECs, epithelial cells, ACTA2+ cells and FRCs. c, Dot plot depicts marker genes used for characterization and assignment of the indicated stromal cell types. Frames highlight marker genes of FRC clusters and the two ACTA2+ clusters (8 and 9). SMC, smooth muscle cell; SkMC, skeletal muscle cell. d,e, Expression patterns of VSMC and FRC gene signatures projected onto UMAPs. f, UpSet plot showing differentially expressed genes shared between VSMCs, PRCs in cluster 8 and FRCs. g,i, Top significantly enriched terms according to gene ontology (GO) enrichment analysis based on differentially expressed genes shared between the indicated cell types. Bar plots show counts of genes assigned to respective cellular processes. h,j, Expression patterns of genes assigned to the indicated cellular processes projected onto UMAPs. scRNA-seq data represent a total of 86,966 CD45−CD235a− stromal cells from n = 12 patients. ECM, extracellular matrix.

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