DNA Methylation Protocols

Front Matter ....Pages i-xviii
Front Matter ....Pages 1-1
 A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation  (Gitte Brinch Andersen, Jörg Tost)....Pages 3-30
 Considerations for Design and Analysis of DNA Methylation Studies  (Karin B. Michels, Alexandra M. Binder)....Pages 31-46
Front Matter ....Pages 47-47
 Quantification of Global DNA Methylation Levels by Mass Spectrometry  (Agustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, Mario F. Fraga)....Pages 49-58
 Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos  (Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings)....Pages 59-80
Front Matter ....Pages 81-81
 Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol  (Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost)....Pages 83-104
 Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing  (Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils et al.)....Pages 105-122
 Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing  (Fumihito Miura, Takashi Ito)....Pages 123-136
 Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection  (William P. Accomando Jr., Karin B. Michels)....Pages 137-159
 Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach  (Julian R. Peat, Sébastien A. Smallwood)....Pages 161-169
 Methyl-CpG-Binding Domain Sequencing: MBD-seq  (Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey A. Shabalin, Edwin J. C. G. van den Oord)....Pages 171-189
 The HELP-Based DNA Methylation Assays  (John M. Greally)....Pages 191-207
 Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq  (Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang)....Pages 209-246
 Digital Restriction Enzyme Analysis of Methylation (DREAM)  (Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu et al.)....Pages 247-265
 Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)  (Fides D. Lay, Theresa K. Kelly, Peter A. Jones)....Pages 267-284
 Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)  (Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, Susan J. Clark)....Pages 285-302
 A Guide to Illumina BeadChip Data Analysis  (Michael C. Wu, Pei-Fen Kuan)....Pages 303-330
Front Matter ....Pages 331-331
 Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing  (H. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, Daniel R. Salomon)....Pages 333-348
 Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)  (Martyna Adamowicz, Klio Maratou, Timothy J. Aitman)....Pages 349-363
 Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes  (Dinh Diep, Nongluk Plongthongkum, Kun Zhang)....Pages 365-382
 Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System  (Jennifer Wendt, Heidi Rosenbaum, Todd A. Richmond, Jeffrey A. Jeddeloh, Daniel L. Burgess)....Pages 383-405
 Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”  (Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, Andreas Weinhaeusel)....Pages 407-424
Front Matter ....Pages 425-425
 Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®  (Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo Glynne Gut, Jörg Tost)....Pages 427-445
 Methylation-Specific PCR  (João Ramalho-Carvalho, Rui Henrique, Carmen Jerónimo)....Pages 447-472
 Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP) Assay  (Mary Jo Fackler, Saraswati Sukumar)....Pages 473-496
 MethyLight and Digital MethyLight  (Mihaela Campan, Daniel J. Weisenberger, Binh Trinh, Peter W. Laird)....Pages 497-513
 Quantitative Region-Specific DNA Methylation Analysis by the EpiTYPER™ Technology  (Sonja Kunze)....Pages 515-535
 Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA)  (Cathy B. Moelans, Lilit Atanesyan, Suvi P. Savola, Paul J. van Diest)....Pages 537-549
 Methylation-Sensitive High Resolution Melting (MS-HRM)  (Dianna Hussmann, Lise Lotte Hansen)....Pages 551-571
 Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes  (Pascal Giehr, Jörn Walter)....Pages 573-586
 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 et al.)....Pages 587-601
Front Matter ....Pages 603-603
 DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation Analysis  (Akram Ghantous, Hector Hernandez-Vargas, Zdenko Herceg)....Pages 605-619
 DNA Methylation Analysis of Free-Circulating DNA in Body Fluids  (Maria Jung, Glen Kristiansen, Dimo Dietrich)....Pages 621-641
Front Matter ....Pages 643-643
 Tet-Assisted Bisulfite Sequencing (TAB-seq)  (Miao Yu, Dali Han, Gary C. Hon, Chuan He)....Pages 645-663
 Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)  (Kristina Kirschner, Felix Krueger, Anthony R. Green, Tamir Chandra)....Pages 665-678
 Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine  (John P. Thomson, Richard R. Meehan)....Pages 679-696
Back Matter ....Pages 697-704