(a) Representative plots of the flow cytometric analysis of FF-AOs treated with CHIR99021 (3 μM), SB431542 (10 μM), their combination (2i), and vehicle control on day 28. Numbers indicate the mean ± s.e.m (n = 3 independent organoids, each). (b) The data of the sequenced reads in SFTPC+ single-cells induced under FF condition with 2i treatment (FF-SFTPC+ cells). (c) The numbers of detected reads of RNA spike-in controls of FF-SFTPC+ single cell lysates. The detected reads (log10) increased according to the number of estimated copies of spike-in controls in each lysate (shown in the text box). Error bars indicate the mean ± 2 s.d. (d) The correlation between the mean expression of each of 24,104 genes in single cells and 200 bulk cells in FF-SFTPC+ cells. r indicates Pearson’s correlation coefficient. (e) The correlation among the mean expression of each of 24,104 genes in FF-SFTPC+ cells, CPMhi progenitor cells on day 21, and SFTPC+ cells induced under fibroblast-dependent condition (FD-SFTPC+ cells) on day 26. r indicates Pearson’s correlation coefficient. (f) Hierarchical clustering analysis of single cell transcriptomes of 85 CPMhi progenitor cells (day 21), 70 FF-SFTPC+ cells, and 50 FD-SFTPC+ cells (GSE90813) based on the representative lung epithelial cell markers described in Supplementary Table 3. B2-3 hiPSC line was used for all of the experiments.