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. 2021 Jun 2;12:3277. doi: 10.1038/s41467-021-23653-4

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© The Author(s) 2021

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. 10 — a Selected ectoderm clusters: FB: forebrain, MB-HB: midbrain–hindbrain, FP: floor plate, SC: spinal cord, NMP: neuromesodermal progenitors, NC: neural crest. b–e (top) UMAP plot and (bottom) spline plot representing changes of expression over pseudotime for marker genes of each cluster: b Nkx1-2 for NMP, c Pax6 for SC, MB-HB, d Cyp26b1 for HB, e Otx2 for FB. f Schematic of the expression pattern of genes expressed in domains of the mouse embryo neural tube along its DV axis. Left: one half of the neural tube in cross-section. From dorsal to ventral: NC: neural crest (outside of the neural tube), RP: roof plate, then arrayed along the DV axis of the neural tube are various progenitor domains: pdl1–pdl6, p0–p2, pMN (motor neuron), p3 then ventrally FP: floor plate. Domains of expression of the markers used to analyse the segregation of cells of neural clusters along AP axis are indicated as bars on the right. g–k Coloured cells expressing specific markers of the dorsal neural tube domain: Wnt1, Msx3; intermediate domain: Dbx2; ventral domain: Olig2, Nkx2-9. l Merge of all cells expressing these five marker genes. m–p Coloured cells expressing specific markers of dorsal domain: Zic1, Pax7, ventral domain: Nkx6-1, Foxa2, q merge of coloured cells expressing these four marker genes. r Position of NC and FP clusters expressing, respectively, Sox10 and Shh. s–u Merge of coloured cells for one dorsal and one ventral markers: s Pax3 (dorsal) and Olig2 (ventral), t Wnt3a (dorsal) and Olig2 (ventral), u Pax6 (dorsal) and Nkx2-9 (ventral). v Summary of clustering of cells expressing dorsal and ventral specific markers, clearly showing the segregation of cell states along the DV axis of the neural tube in a manner similar to what is observed in the mouse embryo.