Fig. 2: Epigenomic signatures of trained and activated monocytes in individuals convalescing from COVID-19.
a, Subclustering UMAP of all monocytes (see Fig. 1c). The five clusters of CD14+ and CD16+ monocytes indicated in the legend were annotated according to sequential differentiation states; cDC, conventional dendritic cells; pDC, plasmacytoid dendritic cells and moDC, monocyte-derived dendritic cells. b, Surface markers overlaid on UMAP embedding coloured according to the log-transformed normalized gene scores. c, Differences in the proportions of clusters 3, 4, 11 and 12 in the samples of individuals convalescing from COVID-19 (COV; n = 8 samples collected from eight individuals, one sample per individual) and healthy donors (HD; n = 4 samples, three samples collected from five HD in this study (including a pooled sample from three HD) and an additional sample from published data (GSE139369)). A two-sided unpaired Student’s t-test was performed to determine the P values. The boxplots denote the median with the quartile range (25–75%), and the length of whiskers represents 1.5× the IQR. d–g, Volcano plots showing the differential TF motif accessibility using the mean TF motif accessibility in the chromVAR TF bias-corrected deviation in clusters 3 and 4 (d), 12 and 11 (e), 13 and 11 (f), and 13 and 12 (g). The P values were calculated using two-sided pairwise Wilcoxon test and the false discovery rate (FDR) was corrected using the Benjamini–Hochberg procedure.
