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. 2022 Oct 6;13:5688. doi: 10.1038/s41467-022-33364-z

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© The Author(s) 2022

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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Fig. 3 — a RNA velocity vector fields and developmental trajectories. Small arrows indicate extrapolated future states of cells. Large arrows indicate branching lineage trajectories constructed using Slingshot and initialized using the origin and end states of the Markov simulation. b The origin and end states of the differentiation landscape determined using Markov random walk simulation on the velocity field. The density of cells at the end of the simulation is shown using the color scale ranging from yellow (low) to blue (high). c Enrichment of early differentiation genes from the EN and IN differentiation trajectories. d–g Smoothed gene expression heatmaps of the top 150 genes differentially expressed along the NP1–NP4 (d), IP-IN–nIN4 (e), NP1–NP3 (f), and IP-EN–nEN1 (g) trajectories. Genes are ordered by peak expression time on the pseudotime axis. Selected genes are listed on the left and shown at the bottom. The top gene ontology terms are listed on the right. h–i UMAP visualization of expression of WNT (h) and BMP/TGFβ (i) signaling pathways genes expression. j Cartoon depicting selected genes and signaling pathways associated with specification of EN and IN lineages in SNR-derived organoids. NP neural progenitor, IP intermediate neural progenitor, nEN newborn excitatory neuron, nIN newborn inhibitory neuron.