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. 2023 Apr 3;42(1):99–108. doi: 10.1038/s41587-023-01728-5

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 2 — (a) RNA velocities predicted by cellDancer are projected onto the spliced-unspliced phase portraits for a set of selected genes. (b) The velocities derived from scVelo dynamic model, DeepVelo, and VeloVAE for gastrulation erythroid maturation cells using MURK genes are visualized on the pre-defined UMAP embedding. Inverted flows from the erythroid 3 to the blood progenitors 2 cell type are observed for the scVelo and DeepVelo predictions; inverted flows from the erythroid 3 to the erythroid 1 cell type are observed for the VeloVAE prediction. (c) Expression pseudotime profiles for four MURK genes Hba-x, Blvrb, Mllt3, and Hbb-y show the expression patterns of transcriptional boost in gastrulation erythroid maturation. (d) Long trajectories used for pseudotime estimation in gastrulation erythroid maturation are visualized on the UMAP embedding. The long trajectories are local maxima of traverse length and are colored from light to dark according to their unadjusted pseudotime. The schematic diagram demonstrates how the unadjusted pseudotime of cells is determined according to the time in the long trajectories. The black bold lines stand for the long trajectories and the pseudotime for the originating cells of the short trajectories (gray lines) is obtained as the time of the closest cell in the corresponding long trajectory.