Fig. 1: Multi-omic analysis of the MFI in patients with COVID-19.

a, Schematic of the experiment design. Frozen tissue samples were pulverized and subjected to RNA extraction for stranded total RNA-seq. The remaining tissue powder underwent nuclei preparation for the following assays: bulk ATAC-seq, snRNA-seq, snATAC-seq and CUT&Tag for H3K27ac and H3K27me3 histone modifications. We then carried out integrative analysis on the multi-omic datasets derived from patient and control MFI samples. b, UMAP of the snRNA-seq showing 21 identified cell types. c, Bubble plot of marker genes for each of the 21 cell types identified in the snRNA-seq. The size of the bubbles represents the percentage of cells within a cluster that expresses the marker gene and the colour of the bubble represents the average expression level of the marker gene calculated by Seurat. d, UMAP of the snATAC-seq showing nine identified cell types. b,d, Each dot represents a nucleus and the colours correspond to its annotated cell type. e, Heatmap of the marker gene scores calculated by ArchR for all nine cell types in the snATAC-seq datasets. Each column represents the gene score of a marker gene and each row represents a cell type. Ctrl, control and Cov, COVID-19; the cell-type abbreviations in c–e are defined in b.