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. 2021 Jul 27;12:4567. doi: 10.1038/s41467-021-24807-0

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© The Author(s) 2021

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a UMAP plot of the macrophage subpopulations in all groups, colored to show cluster information. b Ten different clusters and their specific marker gene expression levels, with brightness indicating log-normalized average expression, and circle size indicating the percent expressed. c Proportion of each macrophage cell type at uninfected control (n = 3), 2 dpi (n = 3), and 5 dpi (n = 4). The height of bars indicates mean and error bars indicate standard deviation. d Heatmap of cluster-specific differentially expressed genes (DEGs), for each macrophage cell type (n = 9). The color indicates the relative gene expression, and representative genes are shown together. e Bar plots showing −log10(p value) from enrichment analysis of representative GO biological pathways among FABP4⁺DDX60⁻ macrophages (resting tissue macrophages), APOE⁺ macrophages, SPP1^hiCHIT1^int M2 (potentially profibrogenic), FABP4⁺DDX60⁺ macrophages (activated tissue macrophages), and DDX60⁺CHIT1^hi macrophages (monocyte-derived infiltrating). The p values are calculated from a theoretical null distribution with a two-sided Wilcoxon signed-rank test. Source data are provided as a Source Data file.