DNA Methylation Protocols

Description

Of the biological processes, disease-associated changes, and clinical applications of DNA methylation / Gitte Brinch Andersen and Jorg Tost -- 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.

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