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Next Generation Sequencing

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Steven R. Head

    1. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Phillip Ordoukhanian

    1. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Daniel R. Salomon

    1. Department of Molecular Medicine, The Scripps Research Institute Center for Organ and Cell Transplantation, La Jolla, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1712)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xiii
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  2. An Integrated Polysome Profiling and Ribosome Profiling Method to Investigate In Vivo Translatome

    • Hyun Yong Jin, Changchun Xiao
    Pages 1-18

  3. Measuring Nascent Transcripts by Nascent-seq

    • Fei Xavier Chen, Stacy A. Marshall, Yu Deng, Sun Tianjiao
    Pages 19-26

  4. Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis

    • Lieselot Deleye, Dieter De Coninck, Dieter Deforce, Filip Van Nieuwerburgh
    Pages 27-42

  5. Multiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure

    • Timokratis Karamitros, Gkikas Magiorkinis
    Pages 43-51

  6. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing

    • Bernard J. Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J. Park
    Pages 53-70

  7. ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras

    • Elizabeth Jaworski, Andrew Routh
    Pages 71-85

  8. Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach

    • Heather J. Lee, Sébastien A. Smallwood
    Pages 87-95

  9. Sequencing of Genomes from Environmental Single Cells

    • Robert M. Bowers, Janey Lee, Tanja Woyke
    Pages 97-111

  10. SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms

    • Phillip A. Morin, Andrew D. Foote, Christopher M. Hill, Benoit Simon-Bouhet, Aimee R. Lang, Marie Louis
    Pages 113-144

  11. CleanTag Adapters Improve Small RNA Next-Generation Sequencing Library Preparation by Reducing Adapter Dimers

    • Sabrina Shore, Jordana M. Henderson, Anton P. McCaffrey
    Pages 145-161

  12. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities

    • Pedro J. Torres, Scott T. Kelley
    Pages 163-173

  13. A Bloody Primer: Analysis of RNA-Seq from Tissue Admixtures

    • Casey P. Shannon, Chen Xi Yang, Scott J. Tebbutt
    Pages 175-201

  14. Next-Generation Sequencing of Genome-Wide CRISPR Screens

    • Edwin H. Yau, Tariq M. Rana
    Pages 203-216

  15. Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells

    • Marie Holt, Anne Costanzo, Louis Gioia, Brian Abe, Andrew I. Su, Luc Teyton
    Pages 217-238

  16. Investigate Global Chromosomal Interaction by Hi-C in Human Naive CD4 T Cells

    • Xiangzhi Meng, Nicole Riley, Ryan Thompson, Siddhartha Sharma
    Pages 239-252

  17. Primer Extension, Capture, and On-Bead cDNA Ligation: An Efficient RNAseq Library Prep Method for Determining Reverse Transcription Termination Sites

    • Phillip Ordoukhanian, Jessica Nichols, Steven R. Head
    Pages 253-261

  18. Back Matter

    Pages 263-266
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Keywords

About this book

This volume covers a wide range of various fields of research, with the common thread being Next Generation Sequencing (NGS) related methods and applications, as well as analysis and interpretation of the data obtained. Chapters guide readers through the highly dynamic processes of translational and transcriptional profiling of a cell, method to detect copy number alterations (CNAs), targeted sequencing applications,  method called “Hi-Plex” to characterize known polymorphic loci, single-cell of DNA or RNA, identify and characterize rare circulating CD4 T cells, and computational pipeline for RNAseq analysis. 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.

Authoritative and practical, Next Generation Sequencing: Methodsand Protocols aims to be useful and informative for further study into this vital field. 

Editors and Affiliations

  • Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, USA

    Steven R. Head, Phillip Ordoukhanian

  • Department of Molecular Medicine, The Scripps Research Institute Center for Organ and Cell Transplantation, La Jolla, USA

    Daniel R. Salomon

Bibliographic Information

  • Book Title: Next Generation Sequencing

  • Book Subtitle: Methods and Protocols

  • Editors: Steven R. Head, Phillip Ordoukhanian, Daniel R. Salomon

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7514-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2018

  • Hardcover ISBN: 978-1-4939-7512-9Published: 10 December 2017

  • Softcover ISBN: 978-1-4939-8507-4Published: 22 June 2018

  • eBook ISBN: 978-1-4939-7514-3Published: 09 December 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 266

  • Number of Illustrations: 10 b/w illustrations, 41 illustrations in colour

  • Topics: Human Genetics

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