Pseudotime analysis reveals trends in surface marker and gene expression for differentiation trajectories. (A) Diffusion map colored by pseudotime trajectories to E, GM, and L fates. Each trajectory starts from an HSC (blue) and ends with a progenitor (red). (B) Changes in surface marker expression and FSC-H through pseudotime for each of the 3 trajectories obtained from the normalized index data. For each trajectory, it is possible to see what cell types are passed through to reach the final cell fate. (C) Normalized expression of genes positively (up) or negatively (down) correlated with the pseudotemporal ordering for each trajectory. Mean normalized expression is plotted with standard deviation. (D) Most significant relevant terms from gene set enrichment analysis for all the trajectories, performed in Enrichr. Terms with an adjusted P value <.05 (using Benjamini-Hochberg correction for multiple testing) were considered significant. The full tables of results can be found in the supplemental Data. MGI, mouse genome informatics.