Fig. 3

Transcriptome analysis of cells incubated with SARS-CoV-2 virus-like particles (VLP). A Bar chart shows relative infectivity as measured by luciferase detection assay (± SD from n = 4 independent experiments, [unpaired two-sided t-test, p-values KR-vs-WT:0.0025 (**), D614G-vs-WT:0.0024 (**), D614G-KR-vs-WT:0.0007 (***), and non-significant between KR and D614G-KR (ns)]). B PCA on transcriptome of HEK293T cell lines (expressing ACE2-TMPRSS2) incubated with four variants (WT, KR, D614G, and D614G-KR) SARS-CoV-2 virus-like particles and control (not incubated). PCA plot is based on normalized all differentially expressed (DE) genes and autoscaling of data was used (n = 3 independent experiments). C Heatmap shows normalized expression of top significant differentially expressed genes (comparing KR versus control) in KR, WT, D614G, D614G-KR VLP incubated, and control HEK293T cell lines (adj p-value < 0.05 and log2 fold-change cutoff ≥ 1.5) (n = 3 independent experiments). D GO-enrichment analysis (top 13 biological processes pathways based on p-value and FDR are shown) of up-regulated genes in KR SARS-CoV-2 VLP incubated cells. The enriched terms display an interconnected network with overlapping gene sets (from the list). Each node represents an enriched term and colored by its p-value from red to blue in ascending order (red shows the smallest p-value). The size of each node corresponds to number of linked genes from the list