Fig. 3: The CytoTRACEKernel recovers temporal gene activation.
From: CellRank 2: unified fate mapping in multiview single-cell data
a,b, UMAP embedding of 31,029 embryoid body cells32, colored by original cluster annotation (CPs, cardiac precursors; EN, endoderm; EPs, epicardial precursors; ESC, embryonic stem cell; Hem., hemangioblast; ME, mesoderm; NC, neural crest; NE, neuroectoderm; NS, neuronal subtypes; Post. EN, posterior endoderm; SMPs, smooth muscle precursors; a, left), embryo stage (E) (a, right) and pseudotimes from the CytoTRACEKernel (b). c, Terminal states inferred using the CytoTRACEKernel. d, UMAP embedding colored by fate probabilities (top) and gene expression of recovered drivers (bottom) of the endoderm lineage. e, Smoothed gene expression along the CytoTRACE pseudotime for the automatically identified top 50 lineage-correlated genes, sorted according to their pseudotime peak. Genes identified in the original publication (left) and known drivers (right)32,33,34 additionally recovered with CellRank 2 are indicated.
