High-throughput next generation sequencing: methods and applications / ed. by Young Min Kwon, S.C.Ricke. - New York: Humana Press; Springer 2011. - xi, 308 p.: ill. - (Methods in molecular biology; 733) (Springer protocols). - Ind.: p.299-308. - ISBN 978-1-61779-088-1; ISSN 1064-3745  Место хранения:   021 | Институт цитологии и генетики CO РАН | Новосибирск | Библиотека

Оглавление / Contents

Preface ......................................................... v Contributors ................................................... ix Part I Genome Sequencing 1 Heikos Single-Molecule Sequencing of Bacterial Genomes ....... 3 Kathleen E. Steinmann, Christopher E. Hart, John F. Thompson, and Patrice M. Milos 2 Whole-Genome Sequencing of Unculturable Bacterium Using Whole-Genome Amplification .................................. 25 Tuichi Hongoh and Atsushi Toyoda Part II Gene Expression Analysis 3 RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System ............................................ 37 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 ................................................. 51 Fatih Ozsolak and Patrice M. Milos 5 Discovery of Bacterial sRNAs by High-Throughput Sequencing ................................................. 63 Jane M. Liu and Andrew Camilli 6 Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform ........................................ 81 Byung-Whi Kong 7 Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications ................................ 93 Zhoutao Chen and Xiaoping Duan Part III Microbial Diversity 8 Integrating High Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities .... 107 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 ........................................ 129 Yan Sun, Randall D. Wolcott, and Scot E. Dowd 10 Pyrosequencing of Chaperonin 60 (срn60) Amplicons as a Means of Determining Microbial Community Composition .... 143 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 ................................... 159 Irene B. Hanning and Steven C. Ricke Part IV Metagenomics 12 Metagenomics .............................................. 173 Jack A. Gilbert, Bonnie Laverock, Ben Temperton, Simon Thomas, Martin Muhling, and Margaret Hughes 13 Metagenomic Analysis of Intestinal Microbiomes in Chickens .................................................. 185 Taejoong Kim and Egbert Mundt 14 Gene Expression Profiling: Metatranscriptomics ............ 195 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 ................... 209 Sandy M.S. Wong, Jeffrey D. Gawronski, David Lapointe, and Brian J. Akerley 16 Determining DNA Methylation Profiles Using Sequencing ..... 223 Suhua Feng, Liudmilla Rubbi, Steven E. Jacobsen, and Matteo Pellegrini Part VI Sequencing Library Preparation 17 Preparation of Next-Generation Sequencing Libraries Using NexteraTM Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition ............................................. 241 Nicholas Caruccio 18 Amplification-Free Library Preparation for Paired-End Illumina Sequencing ....................................... 257 Iwanka Kozarewa and Daniel J. Turner 19 Target-Enrichment Through Amplification of Hairpin- Ligated Universal Targets for Next-Generation Sequencing Analysis .................................................. 267 Pallavi Singh, Rajesh Nayak, and Young Min Kwon 20 96-Plex Molecular Barcoding for the Illumina Genome Analyzer .................................................. 279 Iwanka Kozarewa and Daniel J. Turner Index ........................................................ 299