a The effects of individual components of the 8C medium on the expression of an injury-associated regenerative signature in Hyper-organoids (n = 3 mice). Representative genes are shown on the left. b UMAP visualizations of scRNA-seq data across different organoids. The stem cell clusters and cluster 17 annotated in Fig. 2a are plotted. Colors indicate different organoids: ENR-organoids (orange dots), Hyper-organoids (purple dots), and organoids cultured in 8C minus VPA/EPZ6438 condition (–VE) (green dots). c Expression of the fetal gene signature was overlaid on the UMAP shown in b. Hyper- and –VE/ENR-organoids are separated by the purple and green dotted line. d Integrated analysis of stem cell clusters from different organoids in vitro and the irradiation model in vivo. e Expression of the revival stem cell signature was overlaid on the UMAP shown in d. Hyper- and –VE/ENR-organoids are separated by the orange and blue dotted line. f Trajectory reconstruction of single cells from Hyper-organoids with and without VPA/EPZ6438 treatment. Left panel: pre-branch (blue dots, before bifurcation), successful branch (red dots), and failed branch (green dots). Middle panel: cells from the Hyper-organoids (red dots) and –VE-organoids (green dots) were overlaid on the regenerative trajectory, respectively. Right panel: distribution of homeostatic (green dots), injury-responsive (red dots) Lgr5+ cells, and other cells (gray dots) were overlaid on the regenerative trajectory.