A1 Diffusion curvature of embryonic stem cell differentiation

Left: PHATE visualization of scRNA-seq data color coded by time intervals. Right: PHATE plot colored by diffusion curvature values. We applied diffusion curvature to a single-cell RNA-sequencing dataset of human embryonic stem cells [1]. These cells were grown as embryoid bodies over a period of 27 days, during which they start as human embryonic stem cells and differentiate into diverse cellular lineages including neural progenitors, cardiac progenitors, muscle progenitors, etc. This developmental process is visualized using PHATE in Figure A1 (left), where embryonic cells (at days 0-3, annotated in blue) progressively branch into the two large splits of endoderm (upper split) and ectoderm (lower split around day 6.