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. 2022 Jun 15;41(13):e110600. doi: 10.15252/embj.2022110600

Figure 2. Epigenome profiles and CTCF insulation.

Figure 2

  1. Relative abundance (%) of key histone modifications as measured by mass spectrometry. The point marks the mean while error bars indicate standard errors. Three biological replicates in each cell type were analyzed.
  2. UHC of H3 modification abundances. Numeric suffixes indicate biological replicates.
  3. PCA of average H3 modifications abundances in each cell type.
  4. Chromatin accessibility landscape throughout germline development. (left) ATAC‐seq coverage tracks at a representative locus, with peaks highlighted; (second left) distribution of read counts per each in the union peak set; (second right) H3K4me1 ChIP‐seq coverage tracks at the same locus; (right) Distribution of domain widths for H3K4me1‐enriched regions based on cross‐correlation, as implemented in MCORE.
  5. Partial Pearson correlation matrix for inter‐cell type ATAC‐seq differences against d4c7 mPGCLCs versus differences in other epigenetic signals.
  6. Number of E‐P pairs with ABC score > 0.02 (Fulco et al, 2019). Two biological replicates in each cell type were analyzed.
  7. Cell type insulation ranking. 10 different TAD‐calling algorithms were used to determine the cell types' rank in terms of insulation (gold: most insulated; silver: 2nd most insulated; bronze: 3rd most insulated).
  8. Slope of contact decay (P(s)) curves as a function of genomic separation in log‐log space for the germline, neural induction (Bonev et al, 2017), B cell reprogramming (Stadhouders et al, 2018), and cardiomyocyte differentiation (Zhang et al, 2019) datasets.