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. 2022 Jun 13;24(6):858–871. doi: 10.1038/s41556-022-00932-w

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© The Author(s) 2022

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. 1 — a. Volcano plot showing differential gene expression as detected by RNA-seq between naive and primed hPSCs (n = 3 biologically independent samples). Core pluripotency factors (black) as well as factors specific to each pluripotent state (blue for primed; green for naive) are highlighted. Dashed lines indicate p-value < 0.05 and log₂fold change > 2.5 (two-sided student’s t test). P-values can be found in Supplementary Table 8. b. Chromatin occupancy of all proteins with a potential role in stem cell maintenance in naive and primed hPSCs (n = 3 biologically independent samples). Protein names were collected from AmiGO (http://amigo.geneontology.org/; ‘stem cell maintenance’ GO:0019827)^38,50. The following pluripotency-associated proteins were not detected in our dataset: ASCL2, BMP7, BMPR1A, DAZL, DLL1, ERAS, ESRRB, FANCC, FGF10, FGF4, FGFR1, FOXO3, FZD7, HES1, HES5, HESX1, ID1, ID2, ID3, JAG1, KIT, KLF10, KLF2, LBH, LDB2, LIF, LOXL2, LRP5, MCPH1, MED21, MED27, MMP24, MYC, NANOG, NANOS2, NODAL, NOG, NOTCH2, NR0B1, NR2E1, PADI4, PAX2, PAX8, PELO, PHF19, PIWIL2, PRDM16, PROX1, PRRX1, PTN, RAF1, SETD6, SFPI1, SFRP1, SIX2, SKI, SMO, SOX9, SPI1, TAL1, TBX3, TCF15, TCL1, TERT, TP63, TUT4, WNT7A, WNT9B, ZFP36L2, ZNF322, ZNF358, ZNF706. c. ChEP analysis of differential abundance of chromatin-associated complexes in naive and primed hPSCs (n = 3 biologically independent samples), supplementing Fig. 1d,e. Data are presented as mean values + /- SEM. Dashed lines represent 2-fold change. Asterisks indicate p-value < 0. 05 and fold change > 2 (two-sided student’s t test). Low-change proteins (log2 FC < 0.5) involved in ATP-dependent chromatin remodelling (Fig. 1e) are shown. d. Mass spectrometry analyses of global levels of DNA methylation (green) and DNA hydroxymethylation (purple) in naive and primed hPSCs (n = 3 biologically independent samples) Data are presented as mean values + /- SD. Underlying source data is provided in Source Data Extended Data Fig. 1.

Source data