Gene expression was visualized using two strategies. First, gene expression was mapped directly onto the MDS plot, with grey points indicating no expression and with a white-to-red vector of expression indicating low (nonzero) to high expression. Second, pseudotime and differentiation stage were summarized by binning cells into 40 equally spaced groups and plotting the average metric value for all cells in that bin as one row of a heatmap. Top genes loading on each PC were plotted in this manner. The Pearson correlation between every gene and differentiation stage (across all, early, and late cells) and pseudotime (in all, high diff stage, and low diff stage cells) are included in Table S2.
