Extended Data Fig. 4

mRNA sequencing of lungs from Ly6e wildtype and Ly6e knockout mice that were intranasally infected with 60,000 PFU P.1 SARS-CoV-2 and euthanized 3 days post-infection. Volcano plot summarization of differentially expressed genes (DEGs) between uninfected Ly6e wildtype (n = 6) and Ly6e knockout (n = 4) mice (a), uninfected wildtype (n = 6) and SARS-CoV-2 infected wildtype (n = 7) mice (b), and uninfected knockout (n = 4) and SARS-CoV-2 infected knockout (n=7) mice (c). d, Z-score heatmap of the top 25 DEGs for data summarized in a. e, Gene Ontology (GO) enrichment analysis of transcriptomic data from SARS-CoV-2 infected Ly6e wildtype and Ly6e knockout mice. The abscissa is the ratio of the number of differential genes linked with the GO term to the total number of differential genes. The size of a point represents the number of genes annotated to a specific GO term, and the color from red to purple represents the significant level of the enrichment. Male and female mice were used at an approximately 1 to 1 ratio for these experiments. For a-c, P-values were determined using the negative binomial distribution model and adjusted for multiple hypothesis testing using the Benjamini and Hochberg’s approach for controlling the false discovery rate. P-values for e were determined using hypergeometric distribution and adjusted testing using the Benjamini and Hochberg’s approach for controlling the false discovery rate.