Fig. 3.

Next-generation sequencing analysis of SARS-CoV-2 infection in airway organoid. (A) Flowchart of RNA sequencing data analysis. The major analysis components consist of data quality control and preprocessing, differential expression gene analysis, gene ontology and pathway analysis, and isoform detection and splice junction analysis. (B) The left-hand-side and right-hand-side volcano plots display the results in a comparison analysis between the mock sample and SARS-CoV-2 infected sample at 24 h and 96 h, respectively. Volcano plot representing the DEGs satisfying the criteria of log 2 (fold-change) value > 2 or < -2 and p < 0.05. Red and green symbols indicate significantly upregulated and downregulated genes, respectively. (C) Venn diagram shows that 279 genes were commonly identified at 24 h- and 96 h-exposure to viral infection. Purple circle indicates the number of DEGs identified at 24 h exposure to viral infection compared to the mock sample; Orange circle indicates the number of DEGs identified at 96 h exposure to viral infection compared to the mock sample. (D) The bubble plot showed the gene ontology of the 24 h and 96 h infection-affected genes. (E) The heatmap of the semantic similarity matrix from top-ranking random GO terms in 24 h infection-affected group. (F) Heatmap presents the significance of biological processes in the infected cells after 24 h SARS-CoV-2 infection, which are compared to that after 96 h SARS-CoV-2 infection. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)