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. 2023 Sep 25;42(6):946–959. doi: 10.1038/s41587-023-01931-4

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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. 7 — (a) UMAPs with ‘reprogrammed’, ‘dead-end’ and ‘transition’ fate information projected. Fate cells (Days 12 and 21) were re-clustered and annotated with one of the three fates based on marker gene expression/accessibility, in both modalities independently. (b) Clone-cell embedding UMAPs with expression and accessibility information for key marker genes projected. (c) UMAPs with expression and accessibility information of key dead-end marker genes projected. (d) UMAPs for individual modalities with reprogrammed and dead-end fate information projected. (e,f) Contour plots showing longitudinal tracking of cell fates enabled by CellTag-multi, independently for both scRNA and scATAC.