a Principle component analysis of gene expression in HOs cultured for 9 days (n = 3) and for 13 days (n = 3), and in EBs (n = 3), E9.5 hearts (n = 2), and E11.5 hearts (n = 3). The HOs are located near the hearts. Hemoglobin complex-related genes, including Hbb-y, Hba-x, and Hbb-bh, were excluded from the PCA analysis. b Heat map and hierarchical clustering analyses based on the differentially expressed genes between the in vivo embryonic hearts (E9.5 and E11.5) and the EBs without further culturing. Hbb-y, Hba-x, and Hbb-bh are indicated with asterisks. c Gene expression profiles of representative genes for (i) atrium/ventricle regional markers, (ii) markers during embryonic heart development, (iii) general stem cell markers, (iv) CM markers and (v) markers for other tissues including Foxa2/Sox17 (liver and intestine), Pdx1 (pancreas), Myod1 (skeletal muscle), and Otx2/Tbr1 (central nervous system). d MA plot showing the differentially expressed genes between the HOs and EBs (the y axis indicates the log intensity ratio, and the x axis indicates the mean average of log intensity). Genes with a log2-fold change > 5 are shown in red (396 genes), and those with a log2-fold change <−5 are shown in blue (55 genes). e GO analysis based on the 396 upregulated genes of (d) (P value = from 2.79E−18 to 3.89E−11; two-sided Wald test, log2-fold change > 5, middle panel) and the 55 downregulated genes of (d) (bottom; P value = from 8.14E−20 to 2.21E−11; two-sided Wald test, log2-fold change < −5, bottom panel). Source data are provided as a source data file.