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Table 1 Next-generation sequencing-based methods used in epigenomic studies

From: Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease

Epigenetic modification Method Reference(s)
DNA methylation MethylC-seq [40]
  BS-seq [31]
  MeDIP-seq [33]
  MRE-seq [37]
  MethylCap-seq [30]
  RRBS [41]
Histone post-translational modifications ChIP-seq [22, 42]
Histone variants ChIP-seq [36]
Chromatin modifiers and remodelers ChIP-seq [38, 43]
Chromatin accessibility DNAseI-seq [29]
  FAIRE-seq [35]
  Sono-seq [28]
Nucleosome positioning and turnover MNase-seq [44]
  CATCH-IT [32]
Long-range chromatin interactions Hi-C [39]
  ChIA-PET [34]
Allele-specific chromatin signatures haploChIP [42, 97, 124]
  1. BS-seq, bisulfite sequencing; CATCH-IT, covalent attachment of tags to capture histones and identify turnover; ChIA-PET, chromatin interaction analysis with paired-end tag sequencing; ChIP-seq, chromatin immunoprecipitation sequencing; DNAseI-seq, DNAseI sequencing; FAIRE-seq, formaldehyde-assisted isolation of regulatory elements sequencing; haploChIP, haplotype-specific ChIP; Hi-C, high-throughput chromosome capture; MeDIP-seq, methylated DNA immunoprecipitation sequencing; MethylCap-seq, MethylCap sequencing; MethylC-seq, MethylC sequencing; MNase-seq, micrococcal nuclease sequencing; MRE-seq, methylation-sensitive restriction enzyme sequencing; RRBS, reduced representation bisulfite sequencing; Sono-seq, sonicated chromatin sequencing.