High-throughput next generation sequencing : methods and applications / edited by Young Min Kwon, Steven C. Ricke. — Totowa, N.J. : Humana ; London : Springer [distributor], 2011. – (58.17/M592/v.733)

Contents

    CONTENTS
    
    Preface
    Contributors.
    PART I GENOME SEQUENCING
    1 Helicos Single-Molecule Sequencing of Bacterial Genomes
    2 Whole-Genome Sequencing of Unculturable Bacterium Using Whole-Genome Amplification
    PART II GENE EXPRESSION ANALYSIS
    3 RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System
    4 Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing 51
    5 Discovery of Bacterial sRNAs by High-Throughput Sequencing
    6 Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform 81
    7 Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications 93
    PART III MICROBIAL DIVERSITY
    8 Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities
    9 Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment
    10 Pyrosequencing of Chaperonin-60 (cpn60) Amplicons as a Means of Determining Microbial Community Composition
    11 Prescreening of Microbial Populations for the Assessment of Sequencing Potential
    PART IV METAGENOMICS
    12 Metagenomics
    13 Metagenomic Analysis of Intestinal Microbiomes in Chickens
    14 Gene Expression Profiling: Metatranscriptomics
    PART V SEQUENCE PROFILING FOR FUNCTIONAL ANALYSIS
    15 High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens
    16 Determining DNA Methylation Profiles Using Sequencing 223
    PART VI SEQUENCING LIBRARY PREPARATION
    17 Preparation of Next-Generation Sequencing Libraries Using Nextera Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition
    18 Amplification-Free Library Preparation for Paired-End Illumina Sequencing
    19 Target-Enrichment Through Amplification of Hairpin-Ligated Universal Targets for Next-Generation Sequencing Analysis
    20 96-Plex Molecular Barcoding for the Illumina Genome Analyzer
    Index 299