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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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Fig. 4 — a, Heatmap of genes uniquely enriched across uninduced MEFs or one of the two reprogramming fates on day 3 (false discovery rate (FDR) threshold = 0.05, log fold-change threshold = 0; D3-on: Day 3 on-target destined cells, D3-off: Day 3 off-target destined cells). b, Violin plots of several genes enriched in either off-target (dead-end) destined or on-target (reprogramming) destined cells. c, Heatmap of peaks uniquely enriched across uninduced MEFs or one of the two reprogramming fates on day 3 (FDR threshold = 0.05, log fold-change threshold = 1). Right, annotation of peaks linked to genes (Methods). d, Module scores for genes linked to either on-target or off-target DERs projected onto the clone-cell embedding. e, Top, accessibility browser tracks for each lineage split by day, highlighting peaks linked to late lineage markers (on-target: Aox3; off-target: Col28a1 and Vegfd) showing lineage-specific changes in accessibility on day 3. The Aox3- and Vegfd-linked DERs overlap perfectly with an ENCODE Enhancer-Like Signature (ELS) element, while the Col28a1-linked DER is within 100 bp of an ELS. Bottom, expression levels of the three genes across MEFs and the two reprogramming lineages split by days (Mann–Whitney–Wilcoxon test; two-sided; Bonferroni corrected ****P < 0.0001). f, Heatmap of TF activities uniquely enriched across uninduced MEFs or one of the two reprogramming fates on day 3 (FDR threshold = 0.05, mean difference threshold = 0.5). g, Heatmap showing TF activity (left) and gene expression (right) levels for off-target associated TFs in MEFs and each reprogramming lineage split by time points. TF activity scores show a much stronger lineage bias as compared to gene expression. Box plot definitions for b and e—center point, median; box limits, first and third quartiles; whiskers, up to 1.5× interquartile range; cell numbers—as indicated in Extended Data Fig. 6d.