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Fig. 2 | Genome Biology

Fig. 2

From: NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Fig. 2

NOMe-HiC generates high-quality multi-omics data. a 3D genome concordance with in situ Hi-C in IMR-90 cells. From left to right: 500kb resolution for chromosome 6 (including a comparison of the compartment score with Hi-C), 25kb resolution for chromosome 6 (including a comparison of the insulation score and TADs calls with Hi-C), and 5kb resolution for chromosome 6 (including a comparison of chromatin loop calls with Hi-C). b Methylation concordance with whole-genome bisulfite sequencing (WGBS) at HCG (H=A, C, or T) sites in IMR-90 cells. c Average GCH (H=A, C, or T) methyltransferase footprint levels (left) and HCG methylation levels (right) near PolII binding sites. PolII binding sites are divided into quantiles based on the signal strengths of PolII ChIP-seq in IMR-90 cells. Matched random intervals are randomly chosen from the same chromosome and interval lengths as the intervals in the top 0–25% quantile. d Average GCH methyltransferase footprint level and HCG methylation level around distal CEBPB binding sites in IMR-90 cells. e Scatterplot of concordance of gene expression levels with total RNA-seq levels (ENCODE) in IMR-90 cells. f SNPs concordance with the ground truth SNPs data from Genome in a Bottle (GIAB). The results are compared with the SNPs called from WGS (1000 genome project, phase3 in NA12878). Ti/Tv ratio is also compared

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