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. 2020 Aug 6;11:3924. doi: 10.1038/s41467-020-17834-w

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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 UMAP plot showing three clusters of CD14⁺ monocytes and 1 cluster of CD16⁺ monocytes. Cells are colour-coded by clusters. b Bar plot of the proportion of monocytes in cluster 9 at the severe and remission stages and in healthy control individuals. Source data are provided as a Source Data file. c Heatmap of differentially expressed genes (DEGs) in monocytes from the pairwise comparison between the severe-stage patients, remission-stage patients, and healthy control individuals. d UMAP plots showing the expression of selected cytokines in all monocyte clusters. e, f Box plots of the average expression of genes involved in the signalling pathways regulation of acute inflammatory response (e) and cell chemotaxis (f) in monocytes from the severe stage (n = 912 cells) and remission stage (n = 678 cells) and in healthy control individuals (n = 9719 cells). Centre line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers; P values were calculated using two-sided Wilcoxon rank-sum tests. Source data are provided as a Source Data file. g Heatmap of the area under the curve (AUC) scores of expression regulation by transcription factors (TFs), as estimated using SCENIC. The top-ranked TFs showing the highest difference in expression regulation estimates in monocytes from severe-stage COVID-19 patients are shown. h UMAP plots showing the expression of the ATF3, NFIL3, and HIVEP2 genes in monocytes (top) and the AUC of the estimated regulon activity of the corresponding TFs, predicting the degree of expression regulation of their target genes (bottom).