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. 2022 Aug 12;11:e77848. doi: 10.7554/eLife.77848

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© 2022, Cheng et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 6. — (A) Representative snapshots of balanced Hi-C contact matrices of chromosome 2. Tracks of eigenvector-1 fixed with housekeeping genes are shown below, with A and B compartments shown in red and blue, respectively. (B) Hexbin plot of eigenvector-1 for genomic bins (100 kb) in Stag2^f/y and Stag2^f/y;Nes^Cre oligodendrocytes (OLs). (C) Chromatin bins were classified into four categories based on the eigenvector sign and whether it has switched with a delta bigger than 1.5. AB, changing from compartment A in Stag2^f/y to compartment B in Stag2^f/y;Nes^Cre; BA, from B in Stag2^f/y to A in Stag2^f/y;Nes^Cre; AA, A in both Stag2^f/y and Stag2^f/y;Nes^Cre; BB, B in both Stag2^f/y and Stag2^f/y;Nes^Cre. (D) Boxplot of averaged gene expression change of differentially expressed genes (DEGs) (RNA logFC cutoff of ±0.58) inside each genomic bin. Bins counted: AA, 1646; AB, 56; BA, 69; BB, 910. Red dots represent the mean value. An unpaired Wilcoxon test was used for the statistical analysis. **p < 0.01; ***p < 0.001; ns, not significant. Principal component (E) and similarity (F) analysis performed using the insulation score at 10 kb resolution. (G) Aggregate TAD analysis on the 10 kb merged Hi-C matrices using TADs called from the merged samples of Stag2^f/y at 10 kb resolution.

Figure 6—figure supplement 1. — (A) Representative snapshots of balanced Hi-C contact matrices of chromosome 2. Tracks of eigenvector-1 fixed with housekeeping genes are shown below, with A and B compartments shown in red and blue, respectively. (B) Hexbin plot of eigenvector-1 for genomic bins (100 kb) in Stag2^f/y and Stag2^f/y;Nes^Cre oligodendrocytes (OLs). (C) Chromatin bins were classified into four categories based on the eigenvector sign and whether it has switched with a delta bigger than 1.5. AB, changing from compartment A in Stag2^f/y to compartment B in Stag2^f/y;Nes^Cre; BA, from B in Stag2^f/y to A in Stag2^f/y;Nes^Cre; AA, A in both Stag2^f/y and Stag2^f/y;Nes^Cre; BB, B in both Stag2^f/y and Stag2^f/y;Nes^Cre. (D) Boxplot of averaged gene expression change of differentially expressed genes (DEGs) (RNA logFC cutoff of ±0.58) inside each genomic bin. Bins counted: AA, 1646; AB, 56; BA, 69; BB, 910. Red dots represent the mean value. An unpaired Wilcoxon test was used for the statistical analysis. **p < 0.01; ***p < 0.001; ns, not significant. Principal component (E) and similarity (F) analysis performed using the insulation score at 10 kb resolution. (G) Aggregate TAD analysis on the 10 kb merged Hi-C matrices using TADs called from the merged samples of Stag2^f/y at 10 kb resolution.