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Preface...Table of Contents...Contributing Authors... Part I Introduction 1. A Summary of the Biological Processes, Disease-Associated Changes and Clinical Applications of DNA MethylationGitte Brinch Andersen and Jörg Tost 2. Considerations for Design and Analysis of DNA Methylation StudiesKarin B. Michels and Alexandra M. Binder Part II Global DNA Methylation Levels 3. Quantification of Global DNA Methylation Levels by Mass SpectrometryAgustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, and Mario F. Fraga 4. Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam EmbryosNathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, and Sari Pennings Part III Genome-Wide DNA Methylation Analysis 5. Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq ProtocolChristian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, and Jörg Tost 6. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite SequencingDieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, and Christoph Plass 7. Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing Fumihito Miura and Takashi Ito 8. Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size SelectionWilliam P. Accomando and Karin B. Michels 9. Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging ApproachJulian R. Peat and Sébastien A. Smallwood 10. Methyl-CpG Binding Domain Sequencing: MBD-seq Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey Shabalin, and Edwin J.C.G. van den Oord 11. The HELP-Based AssaysJohn M. Greally 12. Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seqXiaoyun Xing, Bo Zhang, Daofeng Li, and Ting Wang 13. 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 14. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)Fides D. Lay, Theresa K. Kelly, and Peter A. Jones 15. Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, and Susan J. Clarkdiv> 16. A Guide to Illumina BeadChip Data AnalysisMichael C. Wu and Pei-Fen Kuan Part IV Highly Multiplexed Target Regions 17. Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite SequencingH. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, and Daniel R. Salomon 18. Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)Martyna Adamowicz-Brice, Klio Maratou, and Timothy J. Aitman 19. Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock ProbesDinh Diep, Nongluk Plongthonkum, and Kun Zhang 20. Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment SystemJennifer Wendt, Heidi Rosenbaum, Todd Richmond, Jeffrey A. Jeddeloh, and Daniel Burgess 21. Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes « MSRE-qPCR »Gabriel Beikirch, Walter Pulverer, Manuela Hofner, Christa Noehammer, and Andreas Weinhaeusel Part V Locus-Specific DNA Methylation Analysis 22. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo G. Gut, and Jörg Tost 23. Methylation-Specific PCRJoão Ramalho-Carvalho, Rui Henrique, and Carmen Jerónimo 24. Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP)Mary Jo Fackler and Saraswati Sukumar 25. MethyLight and Digital MethyLightMihaela Campan, Daniel J. Weisenberger, Bin Trinh, and Peter W. Laird 26. Quantitative Region-Specific DNA Methylation Analysis by the EPITYPERTM TechnologySonja Kunze 27. Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) Cathy B. Moelans, Lilit Atanesyan, Suivi P. Savola, and Paul J. van Diest 28. Methylation - Sensitive - High Resolution Melting (MS-HRM)Dianna Hussmann and Lise Lotte Hansen 29. Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual ChromosomesPascal Giehr and Jörn Walter 30. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA SequencesSusan M. Mitchell, Keith N. Rand, Zheng-Zhou Xu, Thu Ho, Glenn S. Brown, Jason P. Ross, and Peter L. Molloy Part VI DNA Methylation Analysis of Specific Biological Samples 31. DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation AnalysisAkram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg 32. DNA Methylation Analysis of Free-Circulating DNA in Body FluidsMaria Jung, Glen Kristiansen, and Dimo Dietrich Part VII Hydroxymethylation 33. Tet-Assisted Bisulfite Sequencing (TAB-seq)Miao Yu, Dali Han, Gary C, Won, and Chuan He 34. Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)Kristina Kirschner, Felix Krueger, Anthony R. Green, and Tamir Chandra 35. Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-HydroxymethylcytosineJohn P. Thomson and Richard R. Meehan
Show morePreface...Table of Contents...Contributing Authors... Part I Introduction 1. A Summary of the Biological Processes, Disease-Associated Changes and Clinical Applications of DNA MethylationGitte Brinch Andersen and Jörg Tost 2. Considerations for Design and Analysis of DNA Methylation StudiesKarin B. Michels and Alexandra M. Binder Part II Global DNA Methylation Levels 3. Quantification of Global DNA Methylation Levels by Mass SpectrometryAgustin F. Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, and Mario F. Fraga 4. Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam EmbryosNathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, and Sari Pennings Part III Genome-Wide DNA Methylation Analysis 5. Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq ProtocolChristian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, and Jörg Tost 6. Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite SequencingDieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, and Christoph Plass 7. Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing Fumihito Miura and Takashi Ito 8. Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size SelectionWilliam P. Accomando and Karin B. Michels 9. Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging ApproachJulian R. Peat and Sébastien A. Smallwood 10. Methyl-CpG Binding Domain Sequencing: MBD-seq Karolina A. Aberg, Robin F. Chan, Linying Xie, Andrey Shabalin, and Edwin J.C.G. van den Oord 11. The HELP-Based AssaysJohn M. Greally 12. Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seqXiaoyun Xing, Bo Zhang, Daofeng Li, and Ting Wang 13. 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 14. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)Fides D. Lay, Theresa K. Kelly, and Peter A. Jones 15. Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, and Susan J. Clarkdiv> 16. A Guide to Illumina BeadChip Data AnalysisMichael C. Wu and Pei-Fen Kuan Part IV Highly Multiplexed Target Regions 17. Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite SequencingH. Kiyomi Komori, Sarah A. LaMere, Traver Hart, Steven R. Head, Ali Torkamani, and Daniel R. Salomon 18. Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)Martyna Adamowicz-Brice, Klio Maratou, and Timothy J. Aitman 19. Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock ProbesDinh Diep, Nongluk Plongthonkum, and Kun Zhang 20. Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment SystemJennifer Wendt, Heidi Rosenbaum, Todd Richmond, Jeffrey A. Jeddeloh, and Daniel Burgess 21. Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes « MSRE-qPCR »Gabriel Beikirch, Walter Pulverer, Manuela Hofner, Christa Noehammer, and Andreas Weinhaeusel Part V Locus-Specific DNA Methylation Analysis 22. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing Florence Busato, Emelyne Dejeux, Hafida El abdalaoui, Ivo G. Gut, and Jörg Tost 23. Methylation-Specific PCRJoão Ramalho-Carvalho, Rui Henrique, and Carmen Jerónimo 24. Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP)Mary Jo Fackler and Saraswati Sukumar 25. MethyLight and Digital MethyLightMihaela Campan, Daniel J. Weisenberger, Bin Trinh, and Peter W. Laird 26. Quantitative Region-Specific DNA Methylation Analysis by the EPITYPERTM TechnologySonja Kunze 27. Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) Cathy B. Moelans, Lilit Atanesyan, Suivi P. Savola, and Paul J. van Diest 28. Methylation - Sensitive - High Resolution Melting (MS-HRM)Dianna Hussmann and Lise Lotte Hansen 29. Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual ChromosomesPascal Giehr and Jörn Walter 30. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA SequencesSusan M. Mitchell, Keith N. Rand, Zheng-Zhou Xu, Thu Ho, Glenn S. Brown, Jason P. Ross, and Peter L. Molloy Part VI DNA Methylation Analysis of Specific Biological Samples 31. DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation AnalysisAkram Ghantous, Hector Hernandez-Vargas, and Zdenko Herceg 32. DNA Methylation Analysis of Free-Circulating DNA in Body FluidsMaria Jung, Glen Kristiansen, and Dimo Dietrich Part VII Hydroxymethylation 33. Tet-Assisted Bisulfite Sequencing (TAB-seq)Miao Yu, Dali Han, Gary C, Won, and Chuan He 34. Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)Kristina Kirschner, Felix Krueger, Anthony R. Green, and Tamir Chandra 35. Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-HydroxymethylcytosineJohn P. Thomson and Richard R. Meehan
Show moreA Summary of the Biological Processes, Disease-Associated Changes and Clinical Applications of DNA Methylation.- Considerations for Design and Analysis of DNA Methylation Studies.- Quantification of Global DNA Methylation Levels by Mass Spectrometry.- Antibody Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections and Mammaliam Embryos.- Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol.- Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing.- Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing.- Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection.- Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach.- Methyl-CpG Binding Domain Sequencing: MBD-seq.- The HELP-Based Assays.- Comprehensive Whole DNA Methylome Analysis by InDigital Restriction Enzyme Analysis of Methylation (DREAM).- Nucleosome Occupancy and Methylome Sequencing (NOMe-seq).- Bisulfite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq).- A Guide to Illumina BeadChip Data Analysis.- Microdroplet PCR for Highly-Multiplexed Targeted Bisulfite Sequencing.- Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm).- Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes.- Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System.- Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes MSRE-qPCR.- Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®.- Methylation-Specific PCR.- Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP).- MethyLight and Digital MethyLight.- Quantitative Region-Specific DNA Methylation Analysis by the EPITYPERTM Technology.- Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA).- Methylation - Sensitive - High Resolution Melting (MS-HRM).- Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes.- Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences.- DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation.- DNA Methylation Analysis of Free-Circulating DNA in Body Fluids.- Tet-Assisted Bisulfite Sequencing (TAB-seq).- Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq).- Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine.
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