Affinity-based enrichment techniques for the genome-wide analysis of 5-hydroxymethylcytosine / John P. Thomson and Richard R. Meehan. Considerations for design and analysis of DNA methylation studies / Karin B. Michels and Alexandra M. Binder -- Quantification of global DNA methylation levels by mass spectrometry / Agustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesus Canal, and Mario F. Fraga -- Antibody-based detection of global nuclear DNA methylation in cells, tissue sections, and mammalian embryos / Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, and Sari Pennings -- Whole-genome bisulfite sequencing using the Ovation® ultralow methyl-seq protocol / Christian Daviaud, Victor Renault, Florence Mauger, Jean-Francois Deleuze, and Jorg Tost -- Tagmentation-based library preparation for low DNA input whole genome bisulfite sequencing / Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, and Christoph Plass -- Post-bisulfite adaptor tagging for PCR-free whole-genome bisulfite sequencing / Fumihito Miura and Takashi Ito -- Multiplexed reduced representation bisulfite sequencing with magnetic bead fragment size selection / William P. Accomando Jr. and Karin B. Michels -- Low input whole-genome bisulfite sequencing using a post-bisulfite adapter tagging approach / Julian R. Peat and Sebastien A. Smallwood -- Methyl-CpG-binding domain sequencing : MBD-seq / Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey A. Shabalin, and Edwin J.C.G. van den Oord -- HELP-based DNA methylation assays / John M. Greally -- Comprehensive whole DNA methylome analysis by integrating MeDIP-seq and MRE-seq / Xiaoyun Xing, Bo Zhang, Daofeng Li, and Ting Wang -- Digital restriction enzyme analysis of methylation (DREAM) / Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu, and Jean-Pierre J. Issa -- Nucleosome occupancy and methylome sequencing (NOMe-seq) / Fides D. Lay, Theresa K. Kelly, and Peter A. Jones -- Bisulphite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) / Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, and Susan J. Clark -- Guide to illumina beadChip data analysis / Michael C. Wu and Pei-Fen Kuan -- Microdroplet PCR for highly multiplexed targeted bisulfite sequencing / H. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, and Daniel R. Salomon -- Multiplexed DNA methylation analysis of target regions using microfluidics (fluidigm) / Martyna Adamowicz, Klio Maratou, and Timothy J. Aitman -- Large-scale targeted DNA methylation analysis using bisulfite padlock probes / Dinh Diep, Nongluk Plongthongkum, and Kun Zhang -- Targeted bisulfite sequencing using the seqCap epi enrichment system / Jennifer Wendt, Heidi Rosenbaum, Todd A. Richmond, Jeffrey A. Jeddeloh, and Daniel L. Burgess -- Multiplexed and sensitive DNA methylation testing using methylation-sensitive restriction enzymes "MSRE-qPCR" / Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, and Andreas Weinhaeusel -- Quantitative DNA methylation analysis at single-nucleotide resolution by pyrosequencing / Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo Glynne Gut, and Jorg Tost -- Methylation-specific PCR / Joao Ramalho-Carvalho, Rui Henrique, and Carmen Jeronimo -- Quantitation of DNA methylation by quantitative multiplex methylation-specific PCR (QM-MSP) assay / Mary Jo Fackler and Saraswati Sukumar -- Methylight and digital methyLight / Mihaela Campan, Daniel J. Weisenberger, Binh Trinh, and Peter W. Laird -- Quantitative region-specific DNA methylation analysis by the EpiTYPER technology / Sonja Kunze -- Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) / Cathy B. Moelans, Lilit Atanesyan, Suvi P. Savola, and Paul J. van Diest -- Methylation-sensitive high resolution melting (MS-HRM) / Dianna Hussmann and Lise Lotte Hansen -- Hairpin bisulfite sequencing : synchronous methylation analysis on complementary DNA strands of individual chromosomes / Pascal Giehr and Jorn Walter -- Helper-dependent chain reaction (HDCR) for selective amplification of methylated DNA sequences / Susan M. Mitchell, Keith N. Rand, Zheng-Zhou Xu, Thu Ho, Glenn S. Brown, Jason P. Ross, and Peter L. Molloy -- DNA methylation analysis from blood spots : increasing yield and quality for genome-wide and locus-specific methylation analysis / Akram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg -- DNA methylation analysis of free-circulating DNA in body fluids / Maria Jung, Glen Kristiansen, and Dimo Dietrich -- Tet-assisted bisulfite sequencing (TAB-seq) / Miao Yu, Dali Han, Gary C. Hon, and Chuan He -- Multiplexing for oxidative bisulfite sequencing (oxBS-seq) / Kristina Kirschner, Felix Krueger, Anthony R. Green, and Tamir Chandra -- Affinity-based enrichment techniques for the genome-wide analysis of 5-hydroxymethylcytosine / John P. Thomson and Richard R. Meehan.
Summary:
This third edition volume expands on the previous editions by providing a comprehensive update on the available technologies required to successfully perform DNA methylation analysis. The different technologies discussed in this book analyze the global DNA methylation contents, comprehensive analyses using various NGS based methods for genome-wide DNA methylation analysis, along with precise quantification of DNA methylation levels on single CpG positions. The chapters in this book are divided into 7 parts: an introduction to the field along with tips on study design and data analysis; global DNA methylation levels; genome-wide DNA methylation analysis; highly multiplexed target regions; locus-specific DNA methylation analysis; DNA methylation analysis of specific biological samples; and hydroxymethylation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Series:
Methods in molecular biology, 1064-3745 ; 1708 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.