Extended Data Fig. 2: Quality control and cell-type analysis for samples and multi-omic datasets.
a, Haematoxylin and eosin (top) histological staining and immunostaining of SARS-CoV-2 nucleocapsid protein (bottom) in patients and control tissue. Scale bars, 50 µm. No replicates were performed for the haematoxylin and eosin or N protein immunostaining. b, Principal component analysis (PCA) on the patient samples (n = 7) used in this study based on gene expression from the bulk RNA-seq. The colour of the sample indicates if the pregnancy was carried out to pre-term or term and the shape represents the mode of delivery—either CS or natural delivery. c, DEGs within patient samples when compared according to term of pregnancy (pre-term/term; top) and mode of delivery (CS/natural; bottom). The significance is presented as adjusted two-tailed P value from multiple testing using the Benjamini and Hochberg method (Padj) from DESeq2. Threshold, Padj < 0.05 and log2(fold change) > 1. d, Expression of top marker genes from the snRNA-seq calculated by Seurat. e, Cell-type distribution in all samples from the snRNA-seq after filtering. f, Expression of known SARS-CoV-2 receptors in each cell type from the snRNA-seq calculated by Seurat (bottom). The size of the bubble indicates the percentage of cells in each cell type that expresses the gene. RT–qPCR results of ACE2 and TMPRSS2 in our patient and control samples (top). Each dot represents a sample (n = 7 for both patient and control); P values were calculated using a one-tailed Wilcoxon test. The centre and bounds of boxes indicate the median and quartile of all data points, respectively. The minima and maxima of whiskers indicate quartile 1 − 1.5× the interquartile range and quartile 3 + 1.5× the interquartile range, respectively. g, Gene score of top marker genes from the snATAC-seq calculated by ArchR. h, Cell-type distribution in all samples from the snATAC-seq after filtering.
