Tag-Based Next Generation Sequencing

Description

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.Content: Chapter 1 DeepSuperSAGE: High?Throughput Transcriptome Sequencing with Now? and Next?Generation Sequencing Technologies (pages 1–21): Hideo Matsumura, Carlos Molina, Detlev H. Kruger, Ryohei Terauchi and Prof. Dr. Gunter KahlChapter 2 DeepCAGE: Genome?Wide Mapping of Transcription Start Sites (pages 23–46): Dr. Matthias Harbers, Mitchell S. Dushay and Piero CarninciChapter 3 Definition of Promotome–Transcriptome Architecture Using CAGEscan (pages 47–61): Nicolas Bertin, Charles Plessy, Piero Carninci and Dr. Matthias HarbersChapter 4 RACE: New Applications of an Old Method to Connect Exons (pages 63–71): Charles PlessyChapter 5 RNA?PET: Full?Length Transcript Analysis Using 5?? and 3??Paired?End Tag Next?Generation Sequencing (pages 73–90): Xiaoan Ruan and Yijun RuanChapter 6 Stranded RNA?Seq: Strand?Specific Shotgun Sequencing of RNA (pages 91–108): Alistair R. R. ForrestChapter 7 Differential RNA Sequencing (dRNA?Seq): Deep?Sequencing?Based Analysis of Primary Transcriptomes (pages 109–121): Anne Borries, Jorg Vogel and Cynthia M. SharmaChapter 8 Identification and Expression Profiling of Small RNA Populations Using High?Throughput Sequencing (pages 123–138): Javier Armisen, W. Robert Shaw and Eric A. MiskaChapter 9 Genome?Wide Mapping of Protein–DNA Interactions by ChIP?Seq (pages 139–151): Joshua W. K. Ho, Artyom A. Alekseyenko, Mitzi I. Kuroda and Peter J. ParkChapter 10 Analysis of Protein–RNA Interactions with Single?Nucleotide Resolution Using iCLIP and Next?Generation Sequencing (pages 153–169): Julian Konig, Nicholas J. McGlincy and Jernej UleChapter 11 Massively Parallel Tag Sequencing Unveils the Complexity of Marine Protistan Communities in Oxygen?Depleted Habitats (pages 171–183): Virginia Edgcomb and Thorsten StoeckChapter 12 Chromatin Interaction Analysis Using Paired?End Tag Sequencing (ChIA?PET) (pages 185–210): Xiaoan Ruan and Yijun RuanChapter 13 Tag?Seq: Next?Generation Tag Sequencing for Gene Expression Profiling (pages 211–241): 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 MarraChapter 14 Isolation of Active Regulatory Elements from Eukaryotic Chromatin Using FAIRE (Formaldehyde?Assisted Isolation of Regulatory Elements) (pages 243–255): Paul G. Giresi and Jason D. LiebChapter 15 Identification of Nucleotide Variation in Genomes Using Next?Generation Sequencing (pages 257–276): Hendrik?Jan Megens and Martien A. M. GroenenChapter 16 DGS (Ditag Genome Scanning) – A Restriction?Based Paired?End Sequencing Approach for Genome Structural Analysis (pages 277–285): Jun Chen, Yeong C. Kim and San Ming WangChapter 17 Next?Generation Sequencing of Bacterial Artificial Chromosome Clones for Next?Generation Physical Mapping (pages 287–298): Robert Bogden, Keith Stormo, Jason Dobry, Amy Mraz, Quanzhou Tao, Michiel van Eijk, Jan van Oeveren, Marcel Prins, Jon Wittendorp and Mark van HaarenChapter 18 HELP?Tagging: Tag?Based Genome?Wide Cytosine Methylation Profiling (pages 299–309): Masako Suzuki and John M. GreallyChapter 19 Second?Generation Sequencing Library Preparation: In Vitro Tagmentation via Transposome Insertion (pages 311–321): Fraz SyedChapter 20 Moving Towards Third?Generation Sequencing Technologies (pages 323–336): Karolina Janitz and Michal JanitzChapter 21 Beyond Tags to Full?Length Transcripts (pages 337–352): Mohammed Mohiuddin, Stephen Hutchison and Thomas JarvieChapter 22 Helicos Single?Molecule Sequencing for Accurate Tag?Based RNA Quantitation (pages 353–365): John F. Thompson, Tal Raz and Patrice M. MilosChapter 23 Total RNA?Seq: Complete Analysis of the Transcriptome Using Illumina Sequencing?By?Synthesis Sequencing (pages 367–381): Shujun Luo, Geoffrey P. Smith, Irina Khrebtukova and Gary P. SchrothChapter 24 Computational Infrastructure and Basic Data Analysis for Next?Generation Sequencing (pages 383–392): David SextonChapter 25 CLC Bio Integrated Platform for Handling and Analysis of Tag Sequencing Data (pages 393–405): Roald Forsberg, Soren Monsted and Anne?Mette HeinChapter 26 Multidimensional Context of Sequence Tags: Biological Data Integration (pages 407–416): Korbinian Grote and Thomas WernerChapter 27 Experimental Design and Quality Control of Next?Generation Sequencing Experiments (pages 417–433): 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 DunnenChapter 28 UTGB Toolkit for Personalized Genome Browsers (pages 435–448): Taro L. Saito, Jun Yoshimura, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kurosh and Shinichi MorishitaChapter 29 Beyond the Pipelines: Cloud Computing Facilitates Management, Distribution, Security, and Analysis of High?Speed Sequencer Data (pages 449–468): Boris Umylny and Richard S. J. WeisburdChapter 30 Computational Methods for the Identification of MicroRNAs from Small RNA Sequencing Data (pages 469–475): Eugene Berezikov