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

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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. Representative trunk/thoracic array (array E9.5_2) with highlighted cell states projected spatially. Each dot represents a bead. Outlines are used to emphasize morphological characteristics. A, anterior; P, posterior; D, dorsal; V, ventral. Scale bar, 200 μm b. Comparison of Slide-seq and conventional whole-mount in situ hybridization for gene expression patterns. Spatial gene expression plot showing the expression of Ttn (heart), Sox2 (neural tube), T (tailbud mesoderm), and Meox1 (somites). The color scale depicts normalized gene expression. n/n in the whole-mount in situ hybridization panel indicates the number of embryos exhibiting the pattern to the total number of embryos assayed (from one experiment). Each dot represents a bead. Scale bar, 200 μm. c. Cell states distribution of annotated clusters in the individual E9.5 arrays. Colors represent individual cell states, legend in panel (d). d. Spatial projection of annotated cell states in E9.5 embryo arrays. The panel depicts arrays that cover the trunk/thoracic and head regions. Each color corresponds to a distinct cell state. Each dot represents a bead. Scale bar, 200 μm. A, anterior; P, posterior; D, dorsal; V, ventral; R, rostral; C, caudal. e. Cell state distribution of the annotated clusters in individual arrays of the two independently profiled whole E8.5 stage embryos. Colors represent individual cell states according to the legend in panel (d). f. Cell state distribution of individual states in 10X scRNA-seq reference²⁶ and Slide-seq at E8.5 stage (left panel), and the comparison between the two whole E8.5 embryos profiled by Slide-seq (right panel).