Supplementary Fig. 3: Aberrant DNA methylation in Setd2mNull FGOs. | Nature Genetics

Supplementary Fig. 3: Aberrant DNA methylation in Setd2mNull FGOs.

From: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

Supplementary Fig. 3

a, H3K36me3 staining in control (n = 20) and Setd2mNull FGO (n = 20). A representative image from 3 independent experiments is shown. Scale bars: 20 μm. Quantification of H3K36me3 intensity normalized against DNA staining by Hoechst is also shown. Each dot represents the IF intensity of H3K36me3 in nucleus, with mean value indicated by horizontal lines. Error bar represents s.e.m. P-value (t-test with Welch correlation, two sided) is shown. b, Average plot showing H3K36me3 enrichment at gene body of control (n = 2) and Setd2mNull FGO (n = 2). c-d, EU straining in NSN and SN oocytes in control and Setd2mNull FGO. Diagram showing ratios between NSN and SN in control (n = 52) and Setd2mNull FGO (n = 62) (radius between 70-80 μm). e, α-Tubulin staining in control and Setd2mNull MII oocytes. Arrow shows a polar chromosome. Scale bars: 20 μm. These experiments were performed independently three times. f, Gene expression levels (FPKM) of Dnmts in control (n = 2) and Setd2mNull (n = 2) FGO. Centre line indicates average FPKM value between replicates. Error bar represents s.e.m. g, Averaged 5mC enrichment patterns for chromosome 12 in control and Setd2mNull FGO. Gene desert regions with DNA methylation changes are shaded. h, The numbers of 1-kb bins that gain, lose, or show no changes of DNA methylation in Setd2mNull FGOs. i, Percentages of 1-kb bins that gain, lose, or show no changes of DNA methylation in Setd2mNull FGOs that fall into compartment A/B, respectively. Percentages of whole genome in compartment A/B is shown as a control.

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