Fig. 1.

Multi-tissue and multi-stage scRNAseq data integration of COVID-19 patients and healthy controls. The PBMC dataset was collected from six healthy donors and eight patients separated into moderate and severe COVID-19 conditions, BALF1 and BALF2 from moderate and severe conditions, and the healthy lung dataset from healthy donors. cDC, dendritic cells. A. Overview of the cell types in the integrated single-cell transcriptomes of 37,607 cells derived from COVID-19 patients and healthy controls. Cells are colored by the cell type. B. The cell types in the healthy lung group, PBMC dataset, BALF dataset, and BALF2 dataset. C. The COVID-19 disease conditions in the integrated and D. Separate datasets. Cells are colored according to their COVID-19 condition. The orange color stands for the severe condition where the patients received mechanical ventilation or died from the SARS-CoV-2. The purple color stands for patients diagnosed as COVID-19-positive but only showed mild symptoms. The green color stands for the healthy group. E. The natural log-normalized expression levels of the eight pyroptosis marker genes across cell types, i.e., genes for two caspases: CASP1 and CASP4, two inflammatory cytokines: IL1B and IL18, two membrane damage proteins: NINJ1 and GSDMD, and two pattern recognition receptors: TLR2 and NLRC5.