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Tag-based approaches were originally designed to increase the throughput of capillary sequencing, where concatemers of short sequences were first used in expression profiling. New Next Generation Sequencing methods largely extended the use of tag-based approaches as the tag lengths perfectly match with the short read length of highly parallel sequencing reactions. Tag-based approaches will maintain their important role in life and biomedical science, because longer read lengths are often not required to obtain meaningful data for many applications. Whereas genome re-sequencing and de novo…mehr

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Produktbeschreibung
Tag-based approaches were originally designed to increase the throughput of capillary sequencing, where concatemers of short sequences were first used in expression profiling. New Next Generation Sequencing methods largely extended the use of tag-based approaches as the tag lengths perfectly match with the short read length of highly parallel sequencing reactions. Tag-based approaches will maintain their important role in life and biomedical science, because longer read lengths are often not required to obtain meaningful data for many applications. Whereas genome re-sequencing and de novo sequencing will benefit from ever more powerful sequencing methods, analytical applications can be performed by tag-based approaches, where the focus shifts from 'sequencing power' to better means of data analysis and visualization for common users. Today Next Generation Sequence data require powerful bioinformatics expertise that has to be converted into easy-to-use data analysis tools. The book's intention is to give an overview on recently developed tag-based approaches along with means of their data analysis together with introductions to Next-Generation Sequencing Methods, protocols and user guides to be an entry for scientists to tag-based approaches for Next Generation Sequencing.

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  • Produktdetails
  • Verlag: Wiley-VCH
  • Seitenzahl: 582
  • Erscheinungstermin: 21. Oktober 2011
  • Englisch
  • ISBN-13: 9783527644575
  • Artikelnr.: 37356381
Autorenporträt
Matthias Harbers works in the Japanese biotechnology industry and holds a position as Senior Visiting Scientist at the RIKEN Omics Science Center in Yokohama, Japan. After gaining his PhD at the University Hamburg (Germany), he worked at the Karolinska Institute in Stockholm (Sweden) and the Institut de Génétique et de Biologie Moléculaire et Cellulaire in Strasbourg (France). Main research areas are: -Transcriptome analysis -Preparation of genomic resources -Biomarker discovery Matthias Harbers contributed to advanced scientific publications in high-ranking journals such as Science, PNAS, Nature Genetics, Nature Methods, Journal of Biological Chemistry, Nucleic Acids Research, Genome Research, and Genes and Development among others. Günter Kahl is Professor for Plant Molecular Biology at Frankfurt University, Germany. After his PhD in plant biochemistry, he spent two years with Joe Varner, MSU, East Lansing, and James Bonner, CalTech, Pasadena, USA. Main research areas: -Sequencing and analysis of fungal, plant and animal genomes -Transcriptome analysis in pro- and eukaryotic organisms -Technology development Günter Kahl cooperates with a series of research institutions throughout Europe, in Japan, the USA, Israel, India, and Latin America. He served in expert missions for IAEA, FAO, and UNESCO in many countries, and is presently Chief Scientific Officer in the SME GenXPro GmbH at the Frankfurt Innovation Center Biotechnology.
Inhaltsangabe
TAG
BASED NUCLEIC ACID ANALYSIS DeepSuperSAGE: High
throughput transcriptome sequencing with now
and next
generation sequencing technologies (Hideo Matsumura, Carlos Molina, Detlev H. Krüger, Ryohei Terauchi and Günter Kahl) DeepCAGE: Genome
wide mapping of transcription start sites (Matthias Harbers, Mitch Dushay and Piero Carninci) Definition of promotome
transcriptome architecture using CAGEscan (Nicolas Bertin, Charles Plessy, Piero Carninci and Matthias Harbers) RACE: New applications of an old method to connect exons (Charles Plessy) RNA
PET: Full
Length transcript analysis using 5' and 3' paired
end
tag next generation sequencing (Xiaoan Ruan and Yijun Ruan) Stranded RNA
Seq: Strand specific shotgun sequencing of RNA (Alistair R.R. Forrest) Differential RNA sequencing (dRNA
seq): Deep
sequencing based analysis of primary transcriptomes (Anne Borries, Jörg Vogel and Cynthia M. Sharma) Identification and expression profiling of small RNA populations using high
throughput sequencing (Javier Armisen, W. Robert Shaw and Eric A. Miska) Genome
wide mapping of protein
DNA interactions by ChIP
seq (Joshua W.K. Ho, Artyom A. Alekseyenko, Mitzi I. Kuroda and Peter J. Park) Analysis of protein
RNA interactions with single
nucleotide resolution using iCLIP and next generation sequencing (Julian König, Nicholas J. McGlincy and Jernej Ule) Massively parallel tag sequencing unveils the complexity of marine protistan communities in oxygen
depleted habitats (Virginia Edgcomb and Thorsten Stoeck) Chromatin interaction analysis using paired
end
tag sequencing (ChIA
PET) (Xiaoan Ruan and Yijun Ruan) Tag
seq: Next
generation tag sequencing for gene expression profiling (Sorana Morrissy, Yongjun Zhao, Allen Delaney, Jennifer Asano, Noreen Dhalla, Irene Li, Helen McDonald, Pawan Pandoh, Anna
Liisa Prabhu, Angela Tam, Martin Hirst and Marco Marra) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) (Paul G. Giresi and Jason D. Lieb) Identification of nucleotide variation in genomes using next generation sequencing (Hendrik
Jan Megens and Martien A.M. Groenen) Ditag genome scanning
A restriction
based paired
end sequencing approach for genome structrual analysis (Jun Chen, Yeong C. Kim and San Ming Wang) Next
generation sequencing of BAC clones for next
generation physical mapping (Robert Bogden, Keith Stormo, Jason Dobry, Amy Mraz, Quanzhou Tao, Michiel van Eijk, Jan van Oeveren, Marcel Prins, Jon Wittendorp and Mark van Haaren) HELP
tagging: Tag
based genome
wide cytosine methylation profiling (Masako Suzuki and John M. Greally) Second
generation sequencing library preparation: In vitro tagmentation via transposome insertion (Fraz Syed) NEXT
GENERATION TAG
BASED SEQUENCING Moving towards third
generation sequencing technologies (Karolina Janitz and Michal Janitz) Beyond tags to full
length transcripts (Mohammed Mohiuddin, Stephen Hutchison and Thomas Jarvie) Helicos single
molecule sequencing for accurate tag
based RNA quantitation (John F. Thompson, Tal Raz and Patrice M. Milos) Total RNA
Seq: Complete analysis of the transcriptome using illumina SBS sequencing (Shujun Luo, Geoffrey P. Smith, Irina Khrebtukova and Gary P. Schroth) BIOINFORMATICS FOR TAG
BASED TECHNOLOGIES Computational infrastructure and basic data analysis for next
generation sequencing (David Sexton) The CLC bio integrated platform for handling and analysis of tag sequencing data (Roald Forsberg, Søren Mønsted and Anne
Mette Krabbe Hein) Multi
dimensional context of sequence tags: Biological data integration (Thomas Werner and Korbinian Grote) Experimental design and quality control of next
generation sequencing experiments (Peter A.C. 't Hoen, Matthew S. Hestand, Judith M. Boer, Yuching Lai, Maarten van Iterson, Michiel van Galen, Henk P. Buermans and Johan T. den Dunnen) UTGB toolkit for personalized genome browsers (Taro L. Saito, Jun Yoshimura, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kurosh and Shinichi Morishita) Beyond the pipelines: cloud computing facilitates management, distribution, security and analysis of high speed sequencer data (Boris Umylny and Richard S.J. Weisburd) Computational methods for the identification of microRNAs from small RNA sequencing data (Eugene Berezikov) Web links Glossary