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. 2023 Feb 8;614(7949):742–751. doi: 10.1038/s41586-022-05688-9

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© The Author(s), under exclusive licence to Springer Nature Limited 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 13 — (a,b) t-SNE plot of lhx1a crispant (n = 45,582 cells, 4 biological replicates) and tyr control crispant samples (n = 76,163 cells, 5 biological, 7 technical replicates). (a) Cluster annotation labels transferred from WT reference data projected onto the t-SNE plot. (b) Sample label projected onto the t-SNE plot. (c) Cell cluster composition comparing lhx1a crispant and tyr control crispant samples as a proportion of cells from the whole embryo. (d) Cell density in the axial mesoderm is visualized as a kernel cell density contour plot. The cell number is downsampled to match the cell number before kernel cell density calculation (n = 260, 290, 336, and 367 for lhx1a crispant 1~4, n = 248, 234, 344, 316, 213, 286, and 350 for tyr crispant 1~7). The same contour threshold values are used for the visualization. (e) Cell cluster composition in the axial mesoderm clusters comparing lhx1a crispant and tyr control crispant samples. The left panels show cluster composition in the merged data, while the right panels show the individual scRNA-seq batch. (f) The top 30 NMF module weights for the Early notochord module (left) and the Late notochord module (right) are shown as a bar plot.