title: DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures.
abstract: Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: John P
authors.initials: JP
authors.lastname: Thomson
authors.affiliation: Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.
authors.forename: Angie
authors.initials: A
authors.lastname: Fawkes
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Ottaviano
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Hunter
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Ruchi
authors.initials: R
authors.lastname: Shukla
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Heidi K
authors.initials: HK
authors.lastname: Mjoseng
authors.affiliation: Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Clark
authors.affiliation: Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.
authors.forename: Audrey
authors.initials: A
authors.lastname: Coutts
authors.affiliation: Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.
authors.forename: Lee
authors.initials: L
authors.lastname: Murphy
authors.affiliation: MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Richard R
authors.initials: RR
authors.lastname: Meehan
mesh_terms: D000818:Animals; D004247:DNA; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D055106:Genome-Wide Association Study / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D047468:Immunoprecipitation; D008099:Liver / Q000378:metabolism; D051379:Mice
chemical_list: D004247:DNA