Fig. 4

Differentiated expression state is determined after hiPS cells are seeded for differentiation. a Schematic representation of experimental workflow. Briefly, we transduced hiPS cells at an MOI of ~0.03, allowed them to grow for 3 days (3–4 population doublings), and split them evenly across two parallel cardiac differentiations (split A and split B). On day 14 of differentiation, we performed single-cell RNA sequencing on both splits. We asked whether barcoded clones present in both differentiations were also transcriptionally similar to get at the question of whether cell type determination occurs before or after seeding of hiPS cells for differentiation. b Heatmap of pairwise Jensen-Shannon distances between cells associated with 18 barcodes in split A and the cells associated with the same 18 barcodes in split B. In general, separated clones sharing a barcode (bolded outline along the diagonal) had Jensen-Shannon distances in the same range as clones labeled by distinct barcodes (off the diagonal). c Plots associated with the four featured barcodes outlined in pink in b. Maintaining the organization provided by UMAP, we plotted all cells in the analysis (gray) and recolored cells corresponding to each of the four featured barcodes in two shades of pink corresponding to the two parallel splits. Also for each featured barcode, we plot bar graphs for observed cluster probability distribution in split A (salmon) and the observed cluster probability distribution in split B (magenta)