Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2023 Jul 6;55(7):1176–1185. doi: 10.1038/s41588-023-01435-6

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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/.

PMC Copyright notice

Fig. 3 — a, Schematic of the spatial organization of cell states in the embryonic trunk region at E8.5, and close-up view on the somitogenesis process. b, Schematic and 3D spatial plot of E8.5 (embryo2), showing selected cell states and vISH of Tbx6, Ripply2 and Meox1 in the trunk region. Each dot denotes a bead and the color corresponds to the indicated state. Scale bar, 200 µm. c, UMAP showing beads from E8.5 and E9.5 embryos corresponding to the NMPs, PSM, somites and neural tube states (left) and the corresponding spatial distribution (right) in an E9.5 embryo (array E9.5_2). Each dot denotes a bead and the color corresponds to the indicated state. Scale bar, 100 µm. d, UMAP showing pseudotime analysis along the somitic and neural differentiation trajectories (left) and the corresponding spatial distribution (right) in an E9.5 embryo (array E9.5_2). Each dot denotes a bead and the color corresponds to the assigned pseudotime value. Scale bar, 100 µm. e, Density plot displaying the computed pseudotime difference (y axis) versus the measured spatial distance (x axis) between all beads of the same cell state. Each dot is a pairwise comparison. The dotted line delineates cells with low spatial distance and large transcriptional divergence in the neural tube. f, Spatial plot showing the beads (top) within the dotted line (Fig. 2e) and the distribution of pseudotime values in an E9.5 embryonic trunk (array E9.5_3) that reflects neural tube patterning. Each dot represents a bead. Scale bars, 100 µm.