Extended Data Fig. 9: Pseudotime and spatial analysis of the infected hepatocytes based on Plasmodium transcriptome.

a-d, Monocle UMAP visualization of the infected hepatocytes superimposed with their pseudotime trajectories. Initial node marked with white dot. a, Cells colored by pseudotime value. b, cells colored by sampled time point (hours post infection, hpi). c, Cells colored by their Abortive/Productive tag assigned based on clustering analysis in Fig. 3a. d, Cells colored by the 3 main branching trajectories. e, main UMAP figure colored by the 3 main branching trajectories. Note that branch B3 is in complete overlap with the “Abortive” cell cluster as shown in Extended Data Fig. 8c, while branch B2 is a subset of cluter “Mid-early LS”. f-g, B2 branch is a batch effect of 2 plates with elevated number of reads. f, Heatmap of marker genes per branch. purple – low expression; yellow – high expression. B2 markers are mainly ribosomal genes. g, log10 of total Plasmodium reads is significantly higher in branch B2 compared to B1 (two-sided Wilcoxon rank-sum test). h, Pseudotime distributions in cells binned by cluster. Pairwise significance between consecutive groups was determined by two-sided Wilcoxon rank-sum test (**:p < = 0.01; ****:p < = 0.0001; adjusted p-values for all comparisions p < 2.22e-16; n cells per cluster from left-to-right: 1,657/1,434/507/319/198). bounds of boxes span IQR, horizontal black lines denote the median, whiskers span 1.5*IQR, black-bold circles indicate datapoints outside of said range. i, MA plot (log ratio – M; to max average - A) showing zonally enriched genes in late pseudotime. Y axis indicates log2 of the mean ratio per gene. X axis indicates log10 of the gene’s max average expression. Genes significantly increased pericentral or periportal hepatocytes are plotted in red or blue respectively (FDR q-value < 0.2, Methods). The names of selected genes marked with black circle are highlighted.