Extended Data Fig. 3: Additional scRNAseq analysis.

a-g, ScRNAseq of uninfected cells acquired at 2hpi show increase in genes associated with tissue dissociation. a, Volcano plot of differentially-expressed hepatocyte genes between uninfected cells acquired at 2hpi and at every other time-point. Bold genes are highlighted in (d-f). b, UMAP plot colored by log10 summed relative expression of dissociation marker genes (van den Brink et al. 2017)¹⁷. c, Violin plot of stress indication in uninfected cells binned by time demonstrates notable increase in dissociation stress at 2hpi, both for injection inoculated and mosquito-bitten mice. Bounds of boxes span IQR, horizontal black lines denote the median, whiskers show data within 1.5*IQR. In order from left-to-right, n cells = 3,205/1,445/1,917/2,308/2,838/1,560/3,116/1,632/2,832 over 3/1/4/5/4/3/5/2/3 biologically independent mice. d-e, UMAP plots colored by normalized expression of representative up-regulated genes in the 2hpi cluster. UMAP projections reconstructed based on the combined mouse and Plasmodium transcriptomes. f, smFISH images of Cxcl10 and Mt1 at 2hpi and 24hpi uninfected hepatocyte show no discernible change in expression. Cxcl10 mRNA in red (positive control signal in non-parenchymal cell indicated by white arrow on left panel), Mt1 mRNA in green, Dapi in blue. Images are representatives of 40 imaging fields (15 for 2hpi and 25 for 24hpi) from 4 mice (2 per time point). g, Volcano plot of differentially-expressed hepatocyte genes between mock infected mouse acquired at 2hpi and hepatocytes from uninfected mice. h-i, Host hepatocyte transcriptome changes are also observed in mosquito-bitten mice. h, scatter plot of the log10 mean expression of genes in non-infected hepatocytes (Y axis) vs. infected hepatocytes (X axis) in the mosquito-bitten mice at 36hpi (n = 3 mice). Genes significantly increased or decreased in Fig. 2a are plotted in red or blue respectively. The names of selected genes from Fig. 2a are higlighted. i, Representative smFISH image of genes at 36hpi in mosquito-bitten mouse show similar changes to those observed in injected mice (Fig. 2d). Phalloidin (Phal) in white, Dapi blue; Ftl1 mRNA in red, Apob mRNA in green. Dashed white line - infected hepatocyte; Dotted yellow line - parasite. Image is representative of five imaging fields over two mice.