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. 2019 Mar 14;9:4536. doi: 10.1038/s41598-019-40809-x

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© The Author(s) 2019

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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Distinct cell types in the tissue explants. (a) A tSNE projection of 2,232 cells from tissue explants. Cells are grouped into five clusters based on transcriptome profiles and are colored accordingly. The cell type assignment of each cluster is based on the gene expression analysis. (b) The expression of cluster specific genes, i.e., Col1a1, Epcam, Cd45, Cd68, are displayed on violin plots and tSNE maps. (c) Heatmap shows the expression of top 15 cluster specific genes in 200 cells (or less) from each cluster. Yellow - high expression. Purple - low/no expression. Each row represents a gene, and each column represents a single cell. (d) The top five GO biological processes in macrophage clusters based on the gene enrichment analysis. Top 50 genes in each cluster were included in the analysis. p value was calculated with the Fisher’s Exact Test and adjusted by the Bonferroni correction²⁴. (e) The violin plots of macrophage group specific genes, i.e., Marco, IL18, Arg1, Cxcl3, Cdk1, Stmn1. Every dot represents an individual cell in both violin plots and tSNE maps. The gene expression level is the natural log of the normalized UMI counts in the violin plot. *Bonferroni adjusted p value < 0.001.