References
- Bird A . DNA methylation patterns and epigenetic memory . Genes Dev.16 ( 1 ), 6 – 21 ( 2002 ).
- Law JA , JacobsenSE . Establishing, maintaining and modifying DNA methylation patterns in plants and animals . Nat. Rev. Genet.11 ( 3 ), 204 – 220 ( 2010 ).
- Bergman Y , CedarH . DNA methylation dynamics in health and disease . Nat. Struct. Mol. Biol.20 ( 3 ), 274 – 281 ( 2013 ).
- Bernstein BE , BirneyE , DunhamI , GreenED , GunterC , SnyderM . An integrated encyclopedia of DNA elements in the human genome . Nature489 ( 7414 ), 57 – 74 ( 2012 ).
- Forrest AR , KawajiH , RehliM . A promoter-level mammalian expression atlas . Nature507 ( 7493 ), 462 – 470 ( 2014 ).
- Miura F , EnomotoY , DairikiR , ItoT . Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging . Nucleic Acids Res.40 ( 17 ), e136 ( 2012 ).
- Adey A , ShendureJ . Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing . Genome Res.22 ( 6 ), 1139 – 1143 ( 2012 ).
- Wang Q , GuL , AdeyAet al. Tagmentation-based whole-genome bisulfite sequencing . Nat. Protoc.8 ( 10 ), 2022 – 2032 ( 2013 ).
- Smith ZD , ChanMM , MikkelsenTSet al. A unique regulatory phase of DNA methylation in the early mammalian embryo . Nature484 ( 7394 ), 339 – 344 ( 2012 ).
- Aliotta JM , PelletierJJ , WareJL , MoranLS , BennerJS , KongH . Thermostable Bst DNA polymerase I lacks a 3’‐‐>5’ proofreading exonuclease activity . Genet. Anal.12 ( 5–6 ), 185 – 195 ( 1996 ).
- Yoshida A , NagashimaS , AnsaiTet al. Loop-mediated isothermal amplification method for rapid detection of the periodontopathic bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola . J. Clin. Microbiol.43 ( 5 ), 2418 – 2424 ( 2005 ).
- Xi Y , LiW . BSMAP: whole-genome bisulfite sequence mapping program . BMC Bioinform.10 , 232 ( 2009 ).
- Hansen KD , LangmeadB , IrizarryRA . BSmooth: from whole-genome bisulfite sequencing reads to differentially methylated regions . Genome Biol.13 ( 10 ), R83 ( 2012 ).
- Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences . Nature462 ( 7271 ), 315 – 322 ( 2009 ).
- Gao F , LiuX , WuXPet al. Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis . Genome Biol.13 ( 10 ), R100 ( 2012 ).
- Li X , ZhuJ , HuFet al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression . BMC Genom.13 , 300 ( 2012 ).
- Lister R , O’malleyRC , Tonti-FilippiniJet al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis . Cell133 ( 3 ), 523 – 536 ( 2008 ).
- Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAM tools . Bioinformatics25 ( 16 ), 2078 – 2079 ( 2009 ).
- Smith ZD , ChanMM , MikkelsenTSet al. A unique regulatory phase of DNA methylation in the early mammalian embryo . Nature484 ( 7394 ), 339 – 344 ( 2012 ).
- Wang L , ZhangJ , DuanJet al. Programming and inheritance of parental DNA methylomes in mammals . Cell157 ( 4 ), 979 – 991 ( 2014 ).
- Sébastien AS , HeatherJL , ChristofAet al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity . Nat. Meth.11 ( 8 ), 817 – 820 ( 2014 ).
- NuGEN . www.nugeninc.com/nugen/index.cfm/products/cs/ngs/methyl-seq/ .
- Cutadapt . http://code.google.com/p/cutadapt/ .