Fig 1: Transcriptional Differences of Monocytes from Mild and Severe COVID-19, Related to Figure 4A, Dot plot of the top 10 marker genes sorted by average log fold change of the clusters within the monocyte space of cohort 1 (related to Figure 2, Table S4).B, Gene ontology enrichment analysis based on the complete marker genes obtained for each monocyte cluster of cohort 1, showing the top 10 significant terms enriched in each cluster ranked by adjusted p values.C, Back-mapping of monocyte clusters of cohort 2 (Figure 4C) onto the PBMC UMAP of cohort 2 (Figure 2D). The legend shows the association of the colors to the clusters together with the labeling of the clusters based on expressed marker genes (according to Figures 2 and S3D–S3F).D, Violin plots of marker gene expression in the monocyte clusters identified in the complete PBMC space of cohort 2 (Figures 2C and 2D)E, Dot plot of the top 10 marker genes sorted by average log fold change calculated for the monocyte clusters (Figure 4C).F, Violin plots of the IFI6 and ISG15 expression in cells of mild and severe patients, additionally divided into early (1-10 days after disease onset) and late (> 10 days after disease onset). Statistical analysis was performed using Wilcoxon Rank Sum test adjusted with the Bonferroni method, ****p < 0.0001.G, Violin plots showing the time-dependent change of HLA-DRA and HLA-DRB1 expression in the monocyte population of cohort 1 (mild: n = 4; severe: n = 4) and cohort 2 (mild: n = 5; severe: n = 7). Mild samples are colored in yellow, severe samples in red and controls in blue, with the latter shown as reference violin plots representing the expression of all control monocytes in the respective cohort (cohort 1: n = 22, cohort 2: n = 6).