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Table 1 Summary of experimental approaches for genome-wide DNA methylation profiling

From: Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models

 

aSpecies

bDNA amount

(μg)

Reads

Genome Coverage

(CpG)

cInfluencing factor

Resolution

Bioinformatics requirement

Cost

Array-based methodsd

 MeDIP-chip

limited

5

–

depends on array

A, B, C, D

~ 150 bp

++

++

 MBD-chip

limited

5

–

depends on array

A, B, C, D

~ 150 bp

++

++

 Infinium

limited

0.5–1

–

485 K

C, E, G

Single base

+

+

NGS-based methodse

 MeDIP-seq

any

0.3–5

50 M

~ 23 M

A, B, D

~  150 bp

+++

++

 MBD-seq

any

1–3

30 M

~ 23 M

A, B, D

~  150 bp

+++

++

 RRBS

any

0.01–2

10 M

~ 2 M

E, F, G

Single base

+++

++

 MC-seq

limited

1–3

50 M

3.7 M

E, G

Single base

+++

++

 WGBS

any

1–5

> 500 M

> 28 M

E, G

Single base

+++++

+++++

  1. Abbreviations: MeDIP methylated DNA immunoprecipitation, MBD methyl-CpG-binding domain, NGS next-generation sequencing, RRBS reduced-representation-bisulfite-sequencing, MC-seq methyl-capture sequencing, WGBS whole-genome bisulfite sequencing, M million, K thousand, + very low, ++ low, +++ moderate, ++++ high, +++++ very high
  2. aSpecies: the range of applications varies according to the methylome profiling method adopted; methods are limited to species with commercially available arrays, or species with a complete reference genome available
  3. bDNA input varies depending on the protocol
  4. cInfluencing factors represent the potential sources of genomic region bias. A, CG content; B, CpG density; C, probe hybridization; D, copy number variation; E, bisulfite conversion rate; F, enzyme recognition sites; G, bisulfite PCR bias
  5. dReferences: MeDIP-Chip [39, 40]; MBD-Chip [40, 41]; Infinium [19, 34, 42,43,44]
  6. eReferences: MeDIP-seq [32, 34, 45]; MBD-seq [33, 34, 44, 46]; RRBS [26, 34, 44, 47, 48]; MC-seq [21, 26, 34]; WGBS [20, 26, 34, 44, 49]