Fig. 4

Liver organoid proteomic analysis. a Venn diagram of all identified proteins in all groups. b Principal component analysis of all tested samples. c Heat map of Z-scores from differentially expressed protein IDs in LO after one-way ANOVA test (p < 0.05). d Pathway enrichment analysis using EnrichR related to c. e String interactome graph of protein from the list from c, filtered by most enriched GO biological process, colored differently accordingly to k-means clustering. RT-qPCR for ITGAV and ITGB1 (n = 3, biological replicates, normalized with 2D cultured iPS-derived hepatocyte at day 18 of differentiation protocol; data displayed as great mean and individual scatter plots; one-way ANOVA with Turkey’s post hoc, *p < 0.05 and **p < 0.01). Filtered heat map for TGF, Wnt, and integrin signaling. f Heat map of Z-scores from differentially expressed protein IDs in LO secretome after one-way ANOVA test (p < 0.05). g Pathway enrichment analysis using EnrichR related to f. h String interactome graph of the protein list from f, filtered by most enriched GO biological process and filtered heat map for proteins related to ECM organization and IGF are colored differently accordingly to k-means clustering