Furthermore, as compared to iPSC-KOs, hFKOs show significantly higher expression of early progenitor epithelial genes that are normally expressed mostly in pre-tubular aggregates, RVs, and comma- and S-shaped bodies, such as PAX2, LHX1, and JAG1. Finally, enrichment of Notch pathway-associated gene expression in hFKOs and the critical role of this pathway in nephron patterning enabled us to study the effects of Notch inhibition at the single-cell level and decipher potential developmental defects in Notch-related congenital kidney anomalies, such as those seen in Alagille syndrome. This evidence concerns the gene JAG1 and Alagille syndrome.