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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. 6 — (a) Single-cell quality metrics for the scRNA-seq and scATAC-seq datasets, split by biological replicates. Cell numbers - MEF: 10,119; Rep 1: 92,261 (RNA) and 92,367 (ATAC); Rep 2: 123,827 (RNA) and 121,200 (ATAC). (b) Unique fragments/cell vs single-cell TSS enrichment scatterplots and fragment size distribution plots for the scATAC-seq dataset. (c) Histograms of number of CellTags detected per cell across the two biological replicates after filtering and processing of CellTag reads. (d) Summary of all clones identified across single-cell modalities, for both biological replicates. (e) Venn diagram showing overlap of CellTag signatures across the two biological replicates. (f) UMAPs depicting representative clone nodes from both biological replicates along with their constituent cells. (g) Cells in the clone-cell embedding UMAP with assay information projected shows uniform embedding of both single-cell modalities. (h) UMAP with all clone nodes highlighted shows uniform distribution of clones across all cell states except the unlabeled MEFs.