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. 2023 Oct 21;14:6686. doi: 10.1038/s41467-023-42218-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — 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).