High-Throughput Next Generation Sequencing
(Englisch)
Methods and Applications
Kwon, Young Min & Ricke, Steven C.

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the "next generation sequencing" methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Helicos Single Molecule Sequencing of Bacterial Genomes.- Whole Genome Sequencing of Unculturable Bacterium Using Whole Genome Amplification.- RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System.- Tranillegalscriptome Profiling Using Single-Molecule Direct RNA Sequencing.- Discovery of Bacterial sRNAs by High-Throughput Sequencing.- Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform.- Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications.- Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities.- Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment.- Pyrosequencing of Chaperonin-60 (cpn60) Amplicons as a Means of Determining Microbial Community Composition.- Prescreening of Microbial Populations for the Assessment of Sequencing Potential.- Metagenomics.- Metagenomic Analysis of Intestinal Microbiomes in Chickens.- Gene Expression Profiling: Metatranillegalscriptomics.- High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens.- Determining DNA Methylation Profiles Using Sequencing.- Preparation of Next-Generation Sequencing Libraries Using Nextera(TM) Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition.- Amplification-Free Library Preparation for Paired-End Illumina Sequencing.- Target-Enrichment through Amplification of Hairpin-Ligated Universal Targets for Next-Generation Sequencing Analysis.- 96-Plex Molecular Barcoding for the Illumina Genome Analyzer.

From the reviews:

"This well-illustrated book details the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities, in addition to general applications relevant to the study of any living organism. ... The book is intended for scientists interested in this area, but even graduate students and other researchers field may find this book useful." (Omer Iqbal, Doody's Book Reviews, March, 2012)

Inhaltsverzeichnis

Part I: Genome Sequencing 1. Helicos Single Molecule Sequencing of Bacterial Genomes            Kathleen E. Steinmann, Christopher E. Hart, John F. Thompson, and Patrice M. Milos 2. Whole Genome Sequencing of Unculturable Bacterium Using Whole Genome Amplification            Yuichi Hongoh and Atsushi Toyoda  Part II: Gene Expression Analysis 3. RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System            Tal Raz, Marie Causey, Daniel R. Jones, Alix Kieu, Stan Letovsky, Doron Lipson, Edward Thayer, John F. Thompson, and Patrice M. Milos 4. Tranillegalscriptome Profiling Using Single-Molecule Direct RNA Sequencing            Fatih Ozsolak and Patrice M. Milos 5. Discovery of Bacterial sRNAs by High-Throughput Sequencing            Jane M. Liu and Andrew Camilli 6. Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform            Byung-Whi Kong 7. Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications            Zhoutao Chen and Xiaoping Duan Part III: Microbial Diversity 8. Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities            Husen Zhang, Prathap Parameswaran, Jonathan Badalamenti, Bruce E. Rittmann, and Rosa Krajmalnik-Brown 9. Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment            Yan Sun, Randall D. Wolcott, and Scot E. Dowd 10. Pyrosequencing of Chaperonin-60 (cpn60) Amplicons as a Means of Determining Microbial Community Composition            John Schellenberg, Matthew G. Links, Janet E. Hill, Sean M. Hemmingsen, Geoffrey A. Peters, and Tim J. Dumonceaux 11. Prescreening of Microbial Populations for the Assessment of Sequencing Potential            Irene B. Hanning and Steven C. Ricke Part IV: Metagenomics 12. Metagenomics            Jack A Gilbert, Bonnie Laverock, Ben Temperton, Simon Thomas, Martin Muhling, and Margaret Hughes 13. Metagenomic Analysis of Intestinal Microbiomes in Chickens            Taejoong Kim and Egbert Mundt 14. Gene Expression Profiling: Metatranillegalscriptomics            Jack A. Gilbert and Margaret Hughes Part V: Sequence Profiling for Functional Analysis 15. High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens            Sandy M.S. Wong, Jeffrey D. Gawronski, David Lapointe, and Brian J. Akerley 16. Determining DNA Methylation Profiles Using Sequencing            Suhua Feng, Liudmilla Rubbi, Steven E. Jacobsen, and Matteo Pellegrini Part VI: Sequencing Library Preparation 17. Preparation of Next-Generation Sequencing Libraries Using Nexterä Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition            Nicholas Caruccio 18. Amplification-Free Library Preparation for Paired-End Illumina Sequencing            Iwanka Kozarewa and Daniel J. Turner 19. Target-Enrichment through Amplification of Hairpin-Ligated Universal Targets for Next-Generation Sequencing Analysis            Pallavi Singh, Rajesh Nayak, and Young Min Kwon 20. 96-Plex Molecular Barcoding for the Illumina Genome Analyzer            Iwanka Kozarewa and Daniel J. Turner

Klappentext

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the ¿next generation sequencing¿ methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes.  In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms.  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 key tips on troubleshooting and avoiding known pitfalls.n Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.

Provides techniques necessary to grasp system-wide landscapes of complex molecular events

Supplies practical chapters with easy to follow instructions

Features key tips and implementation advice from the experts