Fig. 5

ScRNA-seq analysis of LSEC populations. a Distribution of LSECs by cell-cycle phase (G1, G2/M, S) and LSEC cluster (11, 12, 13). b Box plot of library size for each LSEC cluster with median library size (top) and graphically denoted median (dark horizontal line). Outliers (black dots) and interquartile range (black box) are indicated. c t-SNE projection of the expression of established LSEC markers in the three identified clusters. c (i) CALCRL c (ii) CD32B, and c (iii) VWF. d Pairwise pathway enrichment analysis of genes DE between clusters 11 and 12 defined in Fig 2f. Pathways enriched in periportal LSECs (Cluster 11) are labeled in red and pathways enriched in central venous LSECs (Cluster 12) are indicated in blue. Colored circles (nodes) represent pathways, sized by number of genes they contain. Green lines depict intra- and inter-pathway relationships according to the number of genes shared between each pathway. Black circles group related pathways into themes that are labeled. e (i) Immunofluorescence of CD32B distribution in liver zone 1 (portal vein - PV), and 2/3 (central vein - CV). CD32B stains mainly LSEC cluster 12 and CK19 stains periportal ductal cells. e (ii, iii, iv, v) are magnified sections corresponding to the indicated roman numerals (white) in (e (i)). e (i) Scale bar represents 200 μm, e (v) scale bar represents 20 μm. Staining was performed on HIER (10 mM Citrate pH 6.0, 95 °C,15 min) treated slides visualized using the matching donkey anti-host antibody and counterstained with DAPI. Slides were scanned and lobules defined as in Supplementary Fig. 10. e (vi) Quantification of percent CD32B positive cells in liver zones 1–3. Error bars show the standard error of the mean for at least 10 replicates. Statistical significance evaluated using a one-way analysis of variance (ANOVA) with a Bonferroni post-test ^∗∗∗P < 0.001, ^∗∗P < 0.01, ^∗P < 0.05. t-SNE: t-distributed stochastic neighbor embedding