References
- Kalari S , PfeiferGP . Identification of driver and passenger DNA methylation in cancer by epigenomic analysis . Adv. Genet.70 , 277 – 308 ( 2010 ).
- Harris RA , WangT , CoarfaCet al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications . Nat. Biotechnol.28 ( 10 ), 1097 – 1105 ( 2010 ).
- Stirzaker C , TaberlayPC , StathamALet al. Mining cancer methylomes: prospects and challenges . Trends Genet.30 ( 2 ), 75 – 84 ( 2014 ).
- Rauch T , PfeiferGP . Methods for assessing genome-wide DNA methylation . In:Handbook of Epigenetics.TollefsbolT ( Ed. ). Elsevier , Amsterdam, The Netherlands , 135 – 147 ( 2010 ).
- Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences . Nature462 ( 7271 ), 315 – 322 ( 2009 ).
- Weber M , DaviesJJ , WittigDet al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells . Nat. Genet.37 ( 8 ), 853 – 862 ( 2005 ).
- Baylin SB , JonesPA . A decade of exploring the cancer epigenome - biological and translational implications . Nat. Rev. Cancer11 ( 10 ), 726 – 734 ( 2011 ).
- De Smet C , LurquinC , LetheBet al. DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter . Mol. Cell. Biol.19 ( 11 ), 7327 – 7335 ( 1999 ).
- Rauch T , LiH , WuXet al. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells . Cancer Res.66 ( 16 ), 7939 – 7947 ( 2006 ).
- Rauch T , PfeiferGP . Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer . Lab. Invest.85 ( 9 ), 1172 – 1180 ( 2005 ).
- Rauch TA , WuX , ZhongXet al. A human B cell methylome at 100-base pair resolution . Proc. Natl Acad. Sci. USA106 ( 3 ), 671 – 678 ( 2009 ).
- Cross SH , CharltonJA , NanXet al. Purification of CpG islands using a methylated DNA binding column . Nat. Genet.6 ( 3 ), 236 – 244 ( 1994 ).
- Hendrich B , BirdA . Identification and characterization of a family of mammalian methyl-CpG binding proteins . Mol. Cell. Biol.18 ( 11 ), 6538 – 6547 ( 1998 ).
- Jiang CL , JinSG , LeeDHet al. MBD3L1 and MBD3L2, two new proteins homologous to the methyl-CpG-binding proteins MBD2 and MBD3: characterization of MBD3L1 as a testis-specific transcriptional repressor . Genomics80 ( 6 ), 621 – 629 ( 2002 ).
- Jiang CL , JinSG , PfeiferGP . MBD3L1 is a transcriptional repressor that interacts with methyl-CpG-binding protein 2 (MBD2) and components of the NuRD complex . J. Biol. Chem.279 ( 50 ), 52456 – 52464 ( 2004 ).
- Choi JH , LiY , GuoJet al. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing . PLoS ONE5 ( 9 ), e13020 ( 2010 ).
- Jin SG , KadamS , PfeiferGP . Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine . Nucleic Acids Res.38 ( 11 ), e125 ( 2010 ).
- Rauch T , WangZ , ZhangXet al. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay . Proc. Natl Acad. Sci. USA104 ( 13 ), 5527 – 5532 ( 2007 ).
- Rauch TA , PfeiferGP . The MIRA method for DNA methylation analysis . Methods Mol. Biol.507 , 65 – 75 ( 2009 ).
- Rauch TA , ZhongX , WuXet al. High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer . Proc. Natl Acad. Sci. USA105 ( 1 ), 252 – 257 ( 2008 ).
- Almamun M , LevinsonBT , GaterSTet al. Genome-wide DNA methylation analysis in precursor B-cells . Epigenetics9 ( 12 ), 1588 – 1595 ( 2014 ).
- Green BB , McKaySD , KerrDE . Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome . BMC Genomics16 ( 1 ), 30 ( 2015 ).
- FastQC . www.bioinformatics.babraham.ac.uk/projects/fastqc/
- FastQ Screen . www.bioinformatics.babraham.ac.uk/projects/fastq_screen
- Langmead B , TrapnellC , PopMet al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biol.10 ( 3 ), R25 ( 2009 ).
- Sam tools . http://sourceforge.net/projects/samtools/files/
- MEDIPS . www.bioconductor.org/packages/2.13/bioc/html/MEDIPS
- Robinson MD , McCarthyDJ , SmythGK . edgeR: a bioconductor package for differential expression analysis of digital gene expression data . Bioinformatics26 ( 1 ), 139 – 140 ( 2010 ).
- Integrative Genomics Viewer . www.broadinstitute.org/igv
- Human Genome Browser Gateway . http://genome.ucsc.edu/cgi-bin/hgGateway
- Hansen KD , LangmeadB , IrizarryRA . BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions . Genome Biol.13 ( 10 ), R83 ( 2012 ).