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. 2023 Oct 20;14:6669. doi: 10.1038/s41467-023-42371-7

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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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Fig. 5 — A UMAP visualization of the mouse Shh single cell clusters obtained after the integration of 3 independant samples. Colors distinguish the different clusters; assigned names are reported at the right of the UMAP. B Violin plots showing the specific marker genes for neuronal clusters. C Regulon specificity score (RSS) for each transcription factor (TF) in Neuronal like clusters. In each cluster, regulons (TF along with their direct targets) are ordered according to their RSS. Interesting regulons are labeled. D Trajectory inference analysis using the PAGA algorithm (Monocle3). Colors distinguish the different clusters as reported in the legend of (A). E Embedding streams (RNA velocity – scVelo) showing the transcriptional dynamics throughout the trajectory. Colors distinguish the different clusters as reported in the legend of (A). F Heatmap showing the gradual expression along the trajectory of: the Notch signaling (Hes, Dlk, Ascl1), the SWI/SNF subunit (Actl6B) and neuronal differentiation gene (Rest, Id, Dcx) expression. Source data are provided as a Source Data file.