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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. 9 — (a) Violin plots comparing accessibility z-scores of FOXA1 and HNF4A genomic binding sites across the two reprogramming fates on Day 3 (Mann Whitney Wilcoxon test, two-sided; p-value: FOXA1 = 1.159e-19, HNF4A = 2.2e-18) suggesting higher on-target binding of the two TFs in the on-target reprogramming lineage on Day 3. (b) Projection of Foxd2 gene expression and FOXD2 TF activity levels on the clone-cell embedding. (c) Bar plots showing fold-change in on-target and off-target marker genes (Cdh1 and Tagln respectively) upon Foxd2 over-expression, compared to a GFP control, on reprogramming day 12 (t-test; p-values: Tagln = 0.006, Cdh1 = 0.03; n=2 biological replicates). (d) Projection of Zfp281 gene expression and ZFP281 TF activity levels on the clone-cell embedding. (e) Tomtom analysis identified four dead-end enriched TFs with significantly similar motifs to ZFP281. ZFP281 shows the highest enrichment in dead-end cells for both gene expression and TF activity levels across all TF candidates. (f) Scatterplot showing correlation between single-cell accessibility of ZFP281 genomic binding sites and ZFP281 motifs (Pearson correlation coefficient = 0.533). (g) Boxplot showing significantly higher cell fate prediction accuracy using ZFP281 target genes (1,612 genes) compared to a size matched set of random genes (Mann Whitney Wilcoxon test, two-sided; p-value = 2.248e-09; n=25 accuracy values/boxplot). (h) Violin plots showing expression levels of Foxd2 and Zfp281 in uninduced MEFs and along the two lineages. All boxplots: center point: median; box limits: first and third quartiles; whiskers: upto 1.5x interquartile range. Panels a and h: Cell numbers – MEF: 10,526; Others – as indicated in Extended Data Fig. 6d.