DNA modifications : methods and protocols /: methods and protocols. (2020)

• Record Type: Book
• Further Information: Note: Edited by Alexey Ruzov, Martin Gering.
• Editors: Ruzov, Alexey; Gering, Martin
• Contents: Part I: Introduction 1. Modified Forms of Cytosine in Eukaryotes: DNA (De)Methylation and Beyond Maria Eleftheriou and Alexey Ruzov 2. Evidence for Non-Cytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An Overview Paige Lowe, Ryszard Olinski, and Alexey Ruzov 3. Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic Ryszard Olinski, Rafal Rozalski, and Daniel Gackowski 4. Mapping DNA Methylation in Mammals: The State of the Art Antonio Lentini and Colm E. Nestor Part II: Detection and Quantification of DNA Modifications Using Mass Spectrometry and Capillary Gel Electrophoresis 5. Detection of Modified Bases in Bacteriophage Genomic DNA Yan-Jiun Lee and Peter R. Weigele 6. Liquid Chromatography–Mass Spectrometry Analysis of Cytosine Modifications Nan Dai and Ivan R. Corrêa Jr. 7. Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS Konstantinos Boulias and Eric Lieberman Greer 8. Quantification of DNA Modifications Using Two-Dimensional Ultra-Performance Liquid Chromatography Tandem Mass-Spectrometry (2D-UPLC–MS/MS) Marta Starczak, Maciej Gawronski, Ryszard Olinski, and Daniel Gackowski 9. MS Analysis of DNA Modifications in Urinary/Body Fluids Aleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski, and Rafal Rozalski 10. Preparation of Internal Standards for 2D-UPLC–MS/MS Quantification of Non-Canonical DNA Bases Marta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski, and Daniel Gackowski 11. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis Romualdas Vaisvila, Lise Hunault, and Lana Saleh Part III: Assessing the Levels and Spatial Distribution of DNA Modifications Using Antibody-Based Approaches 12. Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation Embryos Tie-Bo Zeng and Piroska E. Szabó 13. Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin Garry T. Morgan 14. Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based Immunocytochemistry Abdulkadir Abakir and Alexey Ruzov 15. Immunohistochemical Detection of Modified Cytosine Bases in Rodent Brain Marcus D. Wallis and Rebecca C. Trueman 16. Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish Embryos Peter Jessop and Martin Gering 17. Immunochemical Detection of Modified Species of Cytosine in Plant Tissues Marcos Viejo, Igor Yakovlev, and Carl Gunnar Fossdal 18. Antigen Retrieval for Immunostaining of Modified Cytosine Species Selcen Celik-Uzuner 19. Computational Analysis of DNA Modifications in Confocal Images Seema Rajani, Christopher Gell, Abdulkadir Abakir, and Robert Markus 20. Three-Dimensional Confocal Analysis of Chromosome Positioning Coupled with Immunofluorescence in Mouse Sperm Nuclei Alexandre Champroux, Chantal Goubely, Joëlle Henry-Berger, Joël R. Drevet, and Ayhan Kocer 21. Analysis of 5-Hydroxymethyluracil Levels Using Flow Cytometry Lidia Gackowska, Anna Labejszo, and Daniel Gackowski Part IV: Mapping DNA Modifications 22. Hairpin-Bisulfite PCR Reinhard Stöger 23. Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)–Sequencing Millissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck, and Michael K. Skinner 24. Analysis of 5-Carboxylcytosine Distribution Using DNA Immunoprecipitation Abdulkadir Abakir, Fahad Alenezi, and Alexey Ruzov 25. High Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing Zhijun Huang, Yingying Meng, Piroska E. Szabó, Rahul M. Kohli, and Gerd P. Pfeifer 26. Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol Marie De Borre and Miguel R. Branco 27. Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq) Tong Wang, Meiqi Luo, Kiara N. Berrios, Emily K. Schutsky, Hao Wu, and Rahul M. Kohli 28. Single-Nucleotide-Resolution Sequencing of N6-Methyldeoxyadenosine Wee Siong Sho Goh Part V: Applications of Genome Targeting Methods in Epigenetics 29. Design and Application of DNA Modification-Specific Transcription-Activator-Like Effectors Benjamin Buchmuller, Álvaro Muñoz-López, Mario Gieß, and Daniel Summerer 30. Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic Modifiers Alexander Kondrashov and Elena Karpova Part VI: Analysis of DNA Modifications Sequencing Datasets 31. Analyzing DNA-Immunoprecipitation Sequencing Data Antonio Lentini and Colm E. Nestor 32. Bioinformatics Analysis of DNA Methylation through Bisulfite Sequencing Data Fei Sang 33. Unified Analysis of Multiple ChIP-Seq Datasets Gang Ma, Isaac A. Babarinde, Qiang Zhuang, and Andrew P. Hutchins 34. Integrated Analysis of DNA Methylation, Hydroxymethylation, and Gene Expression Data Using ME-Class2 Manoj K. Singh and John R. Edwards.
• Publisher Details: New York : Humana
• Publication Date: 2020
• Copyright Date: 2021
• Extent: 1 online resource (495 pages)
• Subjects: 660.6/5; Genetic engineering -- Laboratory manuals; DNA -- Laboratory manuals; Genetic Engineering; DNA; DNA; Genetic engineering; Laboratory Manual; Laboratory manuals
• Languages: English
• ISBNs: 9781071608760
• Related ISBNs: 9781071608753
• Access Rights: Legal Deposit; Only available on premises controlled by the deposit library and to one user at any one time; The Legal Deposit Libraries (Non-Print Works) Regulations (UK).
• Access Usage: Restricted: Printing from this resource is governed by The Legal Deposit Libraries (Non-Print Works) Regulations (UK) and UK copyright law currently in force.