Fig. 3: Single-cell transcriptome analysis of hESCs and hESC-QKIdel differentiated cells.
A An UMAP plot shows unsupervised clustering of 19 groups from integrated cell data of differentiated cells at differentiation Day-6 and Day-15. Each cluster is color-coded. The major clusters are to cardiogenic lineages, along with minor clusters of non-cardiogenic lineages. B In the comparison of the distribution of differentiated cells, the overlay of differentiated cells integrated with control H1 and mutant H1-8 cells at Day-6 and Day-15 shows a largely superposable distribution. C, D Representative violin plots show the expression of several key cardiac genes, such as NKX2-5, ISL1, and TBX5, RYR2, PLN, and TNNT2 in each cluster at Day-6 (C) and Day-15 (D), demonstrating dynamic changes of gene expression profile during differentiation. E Monocle 3 analysis of trajectory in pseudotime of cardiogenic lineage cells shows six major cell states from early cardioprogenitors towards differentiated cells, which includes cardioprogenitors, high proliferative cardiomyocytes (hi-Proliferative CMs), differentiating cardiomyocytes (Differentiating CMs), differentiated cardiomyocytes (Differentiated CMs), Endothelial/blood lineage cells, and epicardial lineage cells. Cluster 12 was used as root cells for generating the trajectory of cardiogenic differentiation. F At Day-6, cardioprogenitors, high proliferative cardiomyocytes, and differentiating cardiomyocytes are the major cell types. G Differentiated cardiomyocytes are the major cardiomyocytes at Day-15, accounted for 53.1% and 43.3% in control hESCs (H1)- and hESCs-QKIdel (H1-8)-derived cells, respectively. H Representative scatter plots of average gene expression profiles of differentiated cardiomyocytes (clusters 0 and 4) and differentiating cardiomyocytes (cluster 2) of control H1 versus H1-8 at Day-15. See Supplementary Fig. 6B for respective Reactome Pathway Analysis of clusters 0, 4, and 2.
