Fig. 1

Cardiac directed differentiation of hiPS cells results in extensive heterogeneity of cell expression states. a We directed hiPS cells to differentiate toward cardiac cell types using a well-established monolayer small molecule protocol. b We performed single-cell RNA sequencing on day 14 differentiated cells (n = 17,599 in total after filtering). We applied the UMAP algorithm to the first 50 principal components to visualize differences in gene expression. Cells are colored by clusters determined using Seurat’s FindClusters command at a resolution of 0.5 (i.e., “Seurat clusters, resolution = 0.5”). c Heatmap showing normalized gene expression for 2–3 selected markers per Seurat cluster across all 17,599 cells. Maintaining the organization provided by UMAP, we recolored each cell by its expression of LUM, a fibroblast marker found largely in Seurat clusters 0–2, TNNT2, which marks the putative cardiomyocytes in Seurat cluster 4, ISL1, which marks cardiac progenitors in Seurat cluster 8, WT1, which marks epicardial cells in Seurat cluster 9, and EPCAM, which marks epithelial cells in Seurat cluster 12. d Fraction of variance explained by each of the top 10 principal components for an hiPS cell single-cell RNA sequencing dataset (n = 1,198, top) and for the day 14 differentiated cell dataset. The red line indicates how much variance is explained when the data is randomized prior to PCA (i.e., noise, see “Methods”)