Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

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

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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/.

PMC Copyright notice

Extended Data Fig 8 — (a) Distribution of reprogramming and dead-end destined cells across clusters and (b) their projection on the clone-cell embedding UMAP. (c) CellRank fails to reveal true lineage dynamics underlying reprogramming. Velocity vectors overlaid onto the UMAP (left). ‘Early_1’, a cluster from Day 3 cells identified as a terminal state (middle). Continuous membership values for the terminal state ‘Early_1’ (right). (d) Fate prediction from Day 3 cell state using random forest classifiers. (Mann Whitney Wilcoxon test, two-sided; p-values: Paired vs ATAC = 3.5e-09; Paired vs RNA = 1.4e-09; n=25 accuracy values/boxplot). (e) State-fate prediction analysis using subsets of peaks (Mann Whitney Wilcoxon test, two-sided; p-values: All vs Promoter = 1.757e-08; All vs Exonic = 1.052e-07; n=25 accuracy values/boxplot). (f) Differentially enrichment genes across uninduced MEFs and the two fates on Day 3. (g) Violin plots for several genes enriched in both reprogramming fates on Day 3. (h) DERs are enriched in distal and intronic regions of the genome. (Fischer’s exact test, one-sided; p-values: 0 for both intronic and distal peaks). HOMER analysis to identify motifs enriched in (i) Off-target (dead-end) DERs and (j) On-target (reprogrammed) DERs, compared to a MEF DER background. (k) Enrichment of ENCODE cCRE Enhancer Like Elements in gene linked peaks. (Permutation test, one-sided; 10,000 permutations, p-value: 1e-04). (l) Enrichment of DER linked genes’ module scores in each lineage (Mann Whitney Wilcoxon test, two-sided; p-values: top = 6.2e-221; bottom = 0). (m) Differentially enriched TF activities across uninduced MEFs and the two reprogramming fates on Day 3. (n) Violin plots showing expression of off-target TFs, as identified from TF activity analysis, across uninduced MEFs and the two fates on Day 3. Cdx1 expression was not detected in any of the groups and is hence not plotted (Bonferroni corrected p-values: Cebpb = 1.64e-14, Fosl2 = 1.37e-39). All boxplots: center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range. Panels g, l and n: Cell numbers – MEF: 10,526; Others – as indicated in Extended Data Fig. 6d.