Extended Data Fig. 1: Pathological analysis and transcriptional and proteomic profiles of the lung tissues of patients with COVID-19.
From: A single-cell transcriptomic landscape of the lungs of patients with COVID-19
a, Left, schematic diagram of SARS-CoV-2. Right, representative images of immunostaining of spike glycoprotein (S) in Control (n = 4) and COVID-19 lungs (n = 5 patient lungs sampled from three lung lobes each). Scale bars, 50 μm and 10 μm (zoomed-in images). b, Representative images of H&E staining of Control lungs (n = 4 donors) related to Fig. 1b. Scale bars, 400 μm and 50 μm (zoomed-in images). c, TUNEL staining of lungs. Quantitative data are shown as mean ± s.e.m. Control, n = 13; COVID-19, n = 5 patient lungs sampled from three lung lobes each. Scale bars, 50 μm and 10 μm (zoomed-in image). Two-tailed t-test P values are indicated. d, Bar plot showing the numbers of DEGs and DEPs between Control and COVID-19 groups. e-f, GO term and pathway enrichment analysis of DEGs (e) or DEPs (f) between Control and COVID-19 groups. g, Heatmap showing the overlapped genes of DEGs and DEPs between Control and COVID-19 groups. h-o, Transcriptional, proteomic, and single-nucleus RNA sequencing analyses of Control, COVID-19 and Control-Y groups. Gene set scores of indicated pathway-related genes at RNA and protein levels. P values by Wilcoxon test are indicated (h). Diagram of UPR pathway. Values below indicate log2FC for RNA (left) and protein (right) levels (i). Bar plot showing the reads per cell, sequencing saturation (Top) and cell numbers (Bottom) of each sample in snRNA-seq (j). Box plot showing the detected gene numbers across cells of different samples (k). UMAP plots showing the levels of SFTPB and SFTPC across different cell types before and after the data were processed by CellBender (l). UMAP (m) and box (n) plots showing comparable gene set scores of 19 genes (lung) likely affected by different post-mortem intervals (PMI). UMAP plots showing cell distributions in different samples of human lung tissues (o). Control, n = 4 lungs; COVID-19, n = 5 patient lungs sampled from three lung lobes each; Control-Y, n = 4 lungs. Box shows the median (centre line) and the quartile range (25-75%) and the whiskers extend from the quartiles to the minimum and maximum values. p, Cell numbers of different cell types in human lung tissues.
