Fig. 4.

Single-cell transcriptome analysis of the severe and moderate COVID-19 patients. a Relative expression of the lung-resident memory CD8⁺ T (T_RM) signature genes in T_RM cells and conventional CD8⁺ T cells in moderate patients. b Relative expression of the T_RM featured genes in T_RM cells and conventional CD8⁺ T cells in severe patients. c CXCR6 expression in the T_RM cells of moderate and severe patients. We split the T_RM cells from the annotation of the original paper with 31 marker genes (“Materials and methods”). We conducted a two-sided non-parameter Wilcoxon rank-sum test to test whether CXCR6 was differentially expressed in moderate (red) and severe (blue) groups of T_RM cells. “***” indicates it is genome-wide significant after multiple-test correction of all expressed genes. The small points denote the normalized expression in each cell. Mean normalized expression of CXCR6 in each group is highlighted with the largest circle in black. d Pseudotime inference for the moderate and severe T_RM cells. The red and blue points on t-Distributed Stochastic Neighbor Embedding (tSNE) projection denote the T_RM cells from moderate and severe patients, respectively. The x-axis and y-axis are the first and second dimensions of the tSNE, respectively. e Relative expression of the CXCR6 and naïve and effector T cell markers along the pseudotime proportional to the green color. The gene expressions are scaled by cells. Cells from moderate and severe groups are annotated in blue and red. f Relevance score for hallmark pathways from the molecular signatures database (MSigDB) along the pseudotime. The relevance score (R² coefficient of determination) indicates the proportion of variance in the pseudotime explained by the genes in the hallmark pathways. g Relevance score for transcription factors and their target genes along the pseudotime. The relevance score denotes the proportion of variance in the pseudotime explained by the target genes regulated by the transcription factor