Extended Data Fig. 6: Characterization of differentiated HHOs.
From: Generation of human adult hepatocyte organoids with metabolic functions
a. PCA plotting of HLCs and HPCs with their original cells (modified from Ardisasmita et al.34 Commun Biol). PCA was performed using 5,000 genes with the highest variance as per the original study. Circles represent training data from Ardisasmita et al., while triangles and squares represent the data introduced in this study. The upper right panel illustrates the individual culture conditions of dHHO and eHHOs. b. Expression levels of marker genes in the same PCA coordinates as in Extended Data Fig. 6a. Color code indicates normalized expression levels. c. Expression level of marker genes in the same PCA coordinates as in a. The color code indicates normalized expression levels. d. Expression of genes in the liver-specific gene expression panel (LiGEP). Hierarchical clustering was performed using the Euclidean distance, and the color code indicates a mean-centered log-fold change of log-normalized counts. e. Distance-based similarity scores of different hepatocyte model systems to PHH based on LiGEP expression. Each dot shows the median score of term-related genes by biological replication of cell type and hepatocyte models. From the left, n = 4 (PSC), 4 (Fibroblast) 3 (ICO), 3(CBD), 5(Chol_HLC), 10 (Hep_HPC), 20 (PSC_HLC), 3 (HepG2), 11 (Fib_HLC), 6 (Fetal_Hep), 2 (FHep_HLC), 15(eHHO), 5 (Hep_HLC),18 (dHHO), 5 (Liver), and 29 (PHH). The upper whisker, box top, center, box bottom, and lower whisker of the boxplot shows −(1.5-fold IQR), 25, 50, 75 percentiles, and 1.5-fold IQR, respectively. f. Distance-based similarity scores of different hepatocyte model systems to PHH based on the expression of the indicated gene ontology gene sets related to liver metabolic functions. Each dot shows the median score of term-related genes of one biological replicate. n and boxplot definitions are the same as those in e.
