Fig. 5: Spatial mapping of the granuloma transcriptome.
From: An innate granuloma eradicates an environmental pathogen using Gsdmd and Nos2
a–f Mice were infected with 104 CFU WT C. violaceum and one liver was harvested per indicated timepoint for spatial transcriptomic analysis. a H&E and spatial transcriptomic orientation of indicated clusters from same granuloma at 5 dpi. Spatial transcriptomics was only completed on one experiment. b UMAP plot for cluster expression orientation for all clusters from all timepoints of infection. c UMAP plot of cluster expression in designated locations within granuloma architecture. Necrotic core (NC), necrotic core center (NC-C), necrotic core periphery (NC-P), coagulative necrotic zone (CN), CN-macrophage zone (CN-M), macrophage zone (M), outside granuloma (OG), hepatocyte (HEP), and endothelial cell (EC). d Module scores of various immune cells and fibroblast expression markers from granulomas throughout infection time course. e Indicated cell type expression dot plot in each cluster within the granuloma architecture; combined from all timepoints of infection. f Spatial transcriptomic expression of indicated genes representing immune and non-immune cells within 5 dpi granuloma. S100a9 (neutrophils), Cd68 (macrophages), Ccr2 (monocytes), Trac (T cells), Col1a1 (fibroblasts), and Alb (hepatocytes and endothelial cells).
