Extended Data Fig. 3: Deeper characterization of monocyte/macrophage clusters at early (4 d.p.i.) or late (14 and 28 d.p.i.) SARS-CoV-2 infection (matched to figure 1).
From: Inflammasome activation in infected macrophages drives COVID-19 pathology
a. Heatmap visualizing cluster identifying genes comparing human monocytes and macrophages from infected (4, 14 or 28 d.p.i.) or uninfected lungs (as shown in Fig. 1g). Pooled duplicates. Uninfected: 438 cells, 4 d.p.i.: 336 cells, 14 d.p.i.: 793 cells, 28 d.p.i.: 1368 cells were analysed. This analysis allowed step by step characterization of the inflammatory macrophage response. Marker genes for each cluster of cells were identified using the Wilcoxon rank-sum test (two-tailed) with Seurat. b. Temporal distribution of transcriptional changes associated with monocytes and macrophages in infected (4, 14 or 28 d.p.i.) or uninfected lungs (as shown in Fig. 1g). Pooled duplicates analysed. Uninfected: 438 cells, 4 d.p.i.: 336 cells, 14 d.p.i.: 793 cells, 28 d.p.i.: 1368 cells included in analysis. c. Top: Heatmap of representative genes that are differentially regulated (DEGs) in human macrophages from 4, 14, 28 d.p.i. lungs compared with uninfected lungs. Uninfected: 438 cells, 4 d.p.i.: 336 cells, 14 d.p.i.: 793 cells, 28 d.p.i.: 1368 cells included in analysis. Bottom: Distribution of interferon stimulated genes within these DEGs. Pooled duplicates analysed.
