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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. 3 — (a) Violin plots for single-cell quality metrics for the scRNA-seq and scATAC-seq data. Day 2.5: 5,161 (RNA) and 4,628 (ATAC) cells; Day 5: 56,534 (RNA) and 10,495 (ATAC) cells. (b) Unique fragments/cell vs single-cell TSS enrichment scatterplots and fragment size distribution plot for the two scATAC-seq time-points. (c) scRNA-seq UMAPs with time point (left panel) and cell fate information (right panel) projected. (d) Table summarizing clones identified in scRNA and scATAC datasets independently. (e) RNA fate hierarchy trees built with fewer cells are more discordant with the tree built using the full dataset (n=10 rounds of subsamplings for each indicated cell count). (f) scRNA-seq UMAPs with state and fate siblings for major hematopoietic fates highlighted. (g) Bar plots comparing number of clones and cells in clones across single-modality and joint modality clone calling. (h) Histograms of CellTags detected per cell across scRNA-seq and scATAC-seq datasets after filtering and processing of CellTag reads. (i) Tables summarizing all clones identified in the dataset. (j) Workflow for joint embedding of cells and clone nodes. (k) Top Left: Clone-cell embedding with RNA and ATAC assay information projected (cells only). Top Right and Bottom Left: Comparison of cell embeddings obtained using a conventional FA embedding vs a joint clone-cell graph-based embedding (only cell nodes shown, for direct comparison). Bottom Right: Clone-cell graph FA embedding with cells colored by deviation in their position between the two embeddings. (l) Visualization of clones along with their constituent cells confirms that clone nodes faithfully represent cells. Boxplots in a: center line: median; box limits: first and third quartiles; whiskers: up to 1.5x interquartile range.