Extended Data Fig. 8: Pseudotemporal trajectories derived from scMulTI-Tag in hESC trilineage differentiation.

a) UMAP plot for single cell MulTI-Tag data from projection of H3K27me3 data, with monocle3-derived pseudotemporal trajectories overlaid. Cells are colored by inferred pseudotime. b) UMAP plot describing the same as b) for H3K4me1 data. c) UMAP plot describing the same as a) and b) for a weighted nearest neighbor integration of H3K27me3 and H3K4me1 data. d) monocle3-derived pseudotemporal trajectories for H3K27me3 data, colored by manual annotation of likely correspondence to known differentiation trajectories. e) Same as d) for H3K4me1 data. f) same as d) and e) for a weighted nearest neighbor integration of H3K27me3 and H3K4me1 data. g) Violin plots showing the distribution of inferred pseudotimes derived from H3K27me3 (left) or H3K4me1 (right) data for each cell type profiled. Number of cells profiled for each cell type is denoted at left. h) Pseudotime-ordered heatmaps describing the cell types of the cells assigned to each manually curated trajectory derived from different MulTI-Tag data. Data used to derive each trajectory is displayed at left. For each trajectory, cells are colored by color intensity based on the real assayed differentiation time ranging from hESC (black) to the terminal cell type (mesoderm = green; endoderm = red; ectoderm = blue). Cells assigned to the inferred trajectory that belong to a different trajectory (‘incorrect’) are colored white. For each trajectory-data source combination, inversion rate, defined as the fraction of cell pairs in the trajectory for which the real differentiation time is out of order, and incorrect rate, defined as the fraction of cells assigned to an incorrect trajectory, are displayed at right.