High-Throughput Next Generation Sequencing

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. Transcriptome 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: Metatranscriptomics 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 Nextera(t) 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