Extended Data Fig. 5: Pericentral infected hepatocytes become more abundant at late time points.

a, Violin plots of computationally-inferred zonation scores computed on the scRNAseq data. bounds of boxes span IQR, horizontal black lines denote the median, whiskers span 1.5*IQR (Interquartile range), dashed line demonstrates the median change between groups. Significance determined by two-sided Wilcoxon rank-sum test, with p-value adjusted using Benjamini–Hochberg procedure. b, smFISH of Albumin (Alb, white) and parasite Ch12 18S rRNA (18Sp, green). Yellow squares represents the 40x40 pixels window around the infected cells, number indicates median pixel intensity. Red dots represent the centers of 1248 40x40 pixel windows (“neighborhoods”) randomly placed onto the tissue area. “CV” denotes central-vein locations. Red blow up of 100x100 pixels (11x11 micron) around a pericentral infected cell. Letters indicate the infected cells plotted on c, Histogram of median pixel value of random neighborhoods in the image shown in (b), red X represent values of infected neighborhoods labeled correspondingly to the yellow labels in (b). Note that infected cell ‘C’ resides in a more periportal zone (as evident by the higher Alb levels in its neighborhood). d, smFISH quantification demonstrates lower proportions of infected periportal hepatocytes at 40hpi. Shown is the zonation score based on the smFISH images, namely the probability to observe a neighborhood zonation lower than the value observed in a random cell within the image field. Data points per category represent cells imaged from multiple non-consecutive tissue sections, sampled from 2 biologically independent mice per time point (Methods). e, scRNAseq analysis demonstrates that periportal parasites have lower transcript counts. Cells per time-point (Pericentral/periportal): 2hpi = 69/122, 12hpi = 179/715, 24hpi = 760/692, 30hpi = 182/307, 36hpi = 364/719 taken from 4/5/4/3/5 mice respectively. For (d) and (e), bounds of boxes span IQR, horizontal red lines denote the median, whiskers span 1.5*IQR (Interquartile range), black-bold circles indicate datapoints outside of said range. Significance determined by two-sided Wilcoxon rank-sum test, with p-value adjusted using Benjamini–Hochberg procedure.