Extended Data Fig. 5: Comparison of IFNE or ISG expression in R. aegyptiacus and human organoids, and genetic perturbation of IFNE in bat SIORG.
From: Bat organoids reveal antiviral responses at epithelial surfaces
a, Seurat DotPlot showing the average expression of IFNE and cell type-specific marker genes in the integrated bat nasalALI + bronchialALI (left), or bat SIORG scRNA-seq dataset. Dot size, the percentage of an individual cell type expressing a given marker. Color intensity, the average expression value. Dot sizes were set to a maximum percentage of 50% (genes expressed by more than 50% of cells have the same dot size). b, Seurat DotPlot showing the average expression of ISGs in the bat nasalALI, bronchialALI, alvORG or SIORG scRNA-seq dataset (left), or human nasalALI, bronchialALI or SIORG scRNA-seq dataset (right). Dot size, the percentage of an individual cell type expressing a given marker. Color intensity, the average expression value. c, Violin plots showing the ISG module enrichment score distribution for conserved ISGs (ref. 33) in scRNA-seq of bat or human nasalALI, bronchialALI or SIORG. The distribution was derived from the enrichment scores of individual cells. Median shown as solid line. A positive score indicates enrichment of ISGs in a culture model. Two-sided Mann-Whitney tests were performed to compare human to bat nasalALI, bronchialALI or SIORG (****: P-value < 0.0001). d, Sanger sequencing trace of PCR amplicons spanning the bat IFNE gene in bat SIORG expressing Cas9 and a guide RNA targeting IFNE (sgIFNE) or a non-targeting control guide RNA (sgScrambled). The guide RNA spacer sequence and expected cut site is shown above. e, RT-qPCR analysis of ISGs, normalized to EEF1A1 (2–ΔCT), in Cas9-sgRNA expressing bat SIORG (n = 3). Two-sided unpaired Student’s t-tests were performed to compare ISG expression between sgIFNE-SIORG and sgScrambled-SIORG (**** P < 0.0001). f, VSV titer measured from the culture supernatant of infected sgIFNE (n = 3) or sgScrambled bat SIORG (n = 3) after 8 or 24 hours post infection (hpi). The titer was derived from TCID50 assays performed in VeroE6 cells with five replicates per sample supernatant.
