title: Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing.
abstract: Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes. Furthermore, we provide a brief guideline for base-calling and data analysis of multiplexed RRBS libraries. These strategies will be useful to perform large-scale, genome-wide DNA methylation analysis.
authors.affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. aniruddha.chatterjee@otago.ac.nz.|Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand. aniruddha.chatterjee@otago.ac.nz.
authors.forename: Aniruddha
authors.initials: A
authors.lastname: Chatterjee
authors.affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
authors.forename: Euan J
authors.initials: EJ
authors.lastname: Rodger
authors.affiliation: Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9054, New Zealand.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Stockwell
authors.affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
authors.forename: Gwenn
authors.initials: G
authors.lastname: Le Mée
authors.affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. ian.morison@otago.ac.nz.|Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand. ian.morison@otago.ac.nz.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Morison
mesh_terms: D019295:Computational Biology / Q000379:methods; D018899:CpG Islands; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome; D064878:Web Browser
keywords: CpG island; DMAP; DNA methylation; Epigenetics; Multiplexed; Reduced representation bisulfite sequencing; Second-generation sequencing