Extended Data Fig. 7: RNA velocity and pseudotime analysis in mZ-HLOs.

a) Phase portrait of AFP, GLUL, and GLS2 depicting the dynamics of the gene splicing in the nuclei with the velocity and expression of AFP, GLUL, and GLS2 in nuclei as feature plots. b) SOM (Self Organizing Map) of single-nuclei transcriptome-derived zonation profiles for mZ-HLOs based on the different populations. c) Boxplot showing the pseudotime of each nuclei population in mZ-HLOs. d) Pathway enrichment analysis examining which cellular pathways represented in the hepatoblast, pericentral, periportal, and interzonal hepatocyte populations. Circles (nodes) represent pathways, sized by the number of genes included in that pathway. Related pathways, indicated by light blue lines, are grouped into a theme (black circle) and labeled. Intra-pathway and inter-pathway relationships are shown in light blue and represent the number of genes shared between each pathway. In c data is represented as boxplot where the middle line is the median, the lower and upper hinges correspond to the first and third quartiles, the upper and lower whisker extends from the hinge to the largest and smallest value respectively no further than 1.5 × IQR from the hinge (where IQR is the inter-quartile range), while data beyond the end of the whiskers are outlying points that are plotted individually.