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. 2020 Nov 27;11:6078. doi: 10.1038/s41467-020-19967-4

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© The Author(s) 2020

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. 2 — a Decrease of alveolar macrophages (defined as HLA-DR⁺ CD206⁺ CD163⁺ cells) in the BAL after infection. b Increase in the frequency of myelomonocytic infiltrates (defined as HLA-DR⁺ CD206⁻ CD163⁻) and c of endothelial cells (defined as HLA-DR⁺ CD206⁻ CD163⁺) at infection in BAL (1wk pi). For figure a–c, n = 7, 4, 8, 4 for baseline weeks 1, 2, and 3 time points, respectively, and analyzed by the Kruskal–Wallis test, Dunn’s multiple comparison test. The bars represent mean and standard error. d tSNE plots displaying kinetics of expression of CD16, CD11b, and CD11c markers on live/ HLA-DR⁺ cells populations in BAL before and after infection. e Gating of CD11c⁺ and CD11b⁺ populations on the tSNE map based on antigen expression and discrete density clustering. f Characterization of populations shown in e. The heatmap depicts the fold-change values of each antigen compared to the channel values of negative-expressing cell populations. g Increase in the percentage of CD16⁺ HLA-DR⁺ cells and h in the percentage of interstitial macrophages (CD16⁺ CD206⁻ HLA-DR⁺) expressing of CD11c and i CD11b in BAL overtime (baseline n = 8, week 1 n = 4, week 2 and 3 n = 7; Kruskal–Wallis test, Dunn’s multiple comparisons).