About the Book
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.
Table of Contents:
Preface XIX List of Contributors XXI Part One Tag-Based Nucleic Acid Analysis 1 1 DeepSuperSAGE: High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies 3 Hideo Matsumura, Carlos Molina, Detlev H. Kruger, Ryohei Terauchi, and Gunter Kahl 1.1 Introduction 3 1.2 Overview of the Protocols 5 1.3 Methods and Protocols 9 1.4 Applications 14 1.5 Perspectives 19 References 20 2 DeepCAGE: Genome-Wide Mapping of Transcription Start Sites 23 Matthias Harbers, Mitchell S. Dushay, and Piero Carninci 2.1 Introduction 23 2.2 What is CAGE? 24 2.3 Why CAGE? 26 2.4 Methods and Protocols 28 2.5 Applications 43 2.6 Perspectives 44 References 45 3 Definition of Promotome-Transcriptome Architecture Using CAGEscan 47 Nicolas Bertin, Charles Plessy, Piero Carninci, and Matthias Harbers 3.1 Introduction 47 3.2 What is CAGEscan? 48 3.3 Why CAGEscan? 50 3.4 Methods and Protocols 51 3.5 Applications and Perspectives 59 References 61 4 RACE: New Applications of an Old Method to Connect Exons 63 Charles Plessy 4.1 Introduction 63 4.2 Deep-RACE 65 4.3 Methods Outline 67 4.4 Perspectives 70 References 71 5 RNA-PET: Full-Length Transcript Analysis Using 50- and 30-Paired-End Tag Next-Generation Sequencing 73 Xiaoan Ruan and Yijun Ruan 5.1 Introduction 73 5.2 Methods and Protocols 75 5.3 Applications 88 5.4 Perspectives 90 References 90 6 Stranded RNA-Seq: Strand-Specific Shotgun Sequencing of RNA 91 Alistair R.R. Forrest 6.1 Introduction 91 6.2 Methods and Protocols 93 6.3 Bioinformatic Considerations 103 6.4 Applications 104 6.5 Perspectives 105 References 107 7 Differential RNA Sequencing (dRNA-Seq): Deep-Sequencing-Based Analysis of Primary Transcriptomes 109 Anne Borries, Jorg Vogel, and Cynthia M. Sharma 7.1 Introduction 109 7.2 What is dRNA-Seq? 111 7.3 Why dRNA-Seq? 112 7.4 Methods and Protocols 115 7.5 Applications 119 7.6 Perspectives 120 References 121 8 Identification and Expression Profiling of Small RNA Populations Using High-Throughput Sequencing 123 Javier Armisen, W. Robert Shaw, and Eric A. Miska 8.1 Introduction 123 8.2 HTS/NGS 127 8.3 Methods and Protocols 128 8.4 Troubleshooting 134 8.5 Applications 134 8.6 Perspectives 136 References 138 9 Genome-Wide Mapping of Protein-DNA Interactions by ChIP-Seq 139 Joshua W.K. Ho, Artyom A. Alekseyenko, Mitzi I. Kuroda, and Peter J. Park 9.1 Introduction 139 9.2 Methods and Protocols 141 9.3 Applications 147 9.4 Perspectives 150 References 151 10 Analysis of Protein-RNA Interactions with Single-Nucleotide Resolution Using iCLIP and Next-Generation Sequencing 153 Julian Konig, Nicholas J. McGlincy, and Jernej Ule 10.1 Introduction 153 10.2 Procedure Overview 154 10.3 Antibody and Library Preparation Quality Controls 155 10.4 Oligonucleotide Design 156 10.5 Recent Modifications of the iCLIP Protocol 158 10.6 Troubleshooting 158 10.7 Methods and Protocols 159 References 169 11 Massively Parallel Tag Sequencing Unveils the Complexity of Marine Protistan Communities in Oxygen-Depleted Habitats 171 Virginia Edgcomb and Thorsten Stoeck 11.1 Introduction 171 11.2 Cariaco Basin 173 11.3 Framvaren Fjord 176 11.4 Comparison of Cariaco Basin to Framvaren Fjord 177 11.5 Perspectives on Interpretation of Microbial Eukaryote 454 Data 179 References 182 12 Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) 185 Xiaoan Ruan and Yijun Ruan 12.1 Introduction 185 12.2 Methods and Protocols 192 12.3 Timeline 206 12.4 Anticipated Results 207 12.5 Perspectives 209 References 209 13 Tag-Seq: Next-Generation Tag Sequencing for Gene Expression Profiling 211 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 13.1 Introduction 211 13.2 Protocol Details 212 13.3 Protocol Overview and Timeline 213 13.4 Critical Parameters and Troubleshooting 214 13.5 Methods and Protocols 215 13.6 Applications 239 13.7 Perspectives 240 References 241 14 Isolation of Active Regulatory Elements from Eukaryotic Chromatin Using FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) 243 Paul G. Giresi and Jason D. Lieb 14.1 Introduction 243 14.2 Methods and Protocols 245 14.3 Applications 254 14.4 Perspectives 254 References 255 15 Identification of Nucleotide Variation in Genomes Using Next-Generation Sequencing 257 Hendrik-Jan Megens and Martien A.M. Groenen 15.1 Introduction 257 15.2 Methods 261 15.3 Notes 275 References 275 16 DGS (Ditag Genome Scanning) - A Restriction-Based Paired-End Sequencing Approach for Genome Structural Analysis 277 Jun Chen, Yeong C. Kim, and San Ming Wang 16.1 Introduction 277 16.2 Methods and Protocols 278 16.3 Applications 283 16.4 Perspectives 284 References 285 17 Next-Generation Sequencing of Bacterial Artificial Chromosome Clones for Next-Generation Physical Mapping 287 Robert Bogden, Keith Stormo, Jason Dobry, Amy Mraz, Quanzhou Tao, Michiel van Eijk, Jan van Oeveren, Marcel Prins, Jon Wittendorp, and Mark van Haaren 17.1 History of the Bacterial Artificial Chromosome Vector Systems 287 17.2 History of Physical Mapping 288 17.3 What is WGP? 289 17.4 Flow of a WGP Project 289 17.5 BAC Pooling Strategies 290 17.6 Methods and Protocols 291 17.7 Applications 294 17.8 Perspectives 296 References 297 18 HELP-Tagging: Tag-Based Genome-Wide Cytosine Methylation Profiling 299 Masako Suzuki and John M. Greally 18.1 Introduction 299 18.2 Genome-Wide DNA Methylation Analysis 299 18.3 What is HELP-Tagging? 300 18.4 Methods and Protocols 301 18.5 Applications 308 18.6 Perspectives 308 References 309 19 Second-Generation Sequencing Library Preparation: In Vitro Tagmentation via Transposome Insertion 311 Fraz Syed 19.1 Introduction 311 19.2 Methods and Protocols 313 19.3 Perspectives 321 References 321 Part Two Next-Generation Tag-Based Sequencing 323 20 Moving Towards Third-Generation Sequencing Technologies 325 Karolina Janitz and Michal Janitz 20.1 Introduction 325 20.2 Differences Between NGS and Sanger Sequencing 326 20.3 Preparation of Templates for Sequencing 326 20.4 Real-Time Sequencing 327 20.5 Nanopore Sequencing 328 20.6 Ion Torrent Electronic Sequencing 329 20.7 Genome Enrichment 331 20.8 Advantages of NGS 331 20.9 Problem of Short Reads 333 20.10 Perspectives 335 References 335 21 Beyond Tags to Full-Length Transcripts 337 Mohammed Mohiuddin, Stephen Hutchison, and Thomas Jarvie 21.1 Introduction 337 21.2 Generation of Full-Length Transcriptomes 338 21.3 Methods 342 21.4 Applications 344 21.5 Perspectives 350 References 351 22 Helicos Single-Molecule Sequencing for Accurate Tag-Based RNA Quantitation 353 John F. Thompson, Tal Raz, and Patrice M. Milos 22.1 Introduction 353 22.2 Methods and Protocols 355 22.3 Applications 362 22.4 Perspectives 364 References 365 23 Total RNA-seq: Complete Analysis of the Transcriptome Using Illumina Sequencing-by-Synthesis Sequencing 367 Shujun Luo, Geoffrey P. Smith, Irina Khrebtukova, and Gary P. Schroth 23.1 Introduction 367 23.2 Total RNA-Seq 368 23.3 Methods and Protocols 369 23.4 Total RNA-Seq Data Collection and Interpretation 378 23.5 Applications 380 References 381 Part Three Bioinformatics for Tag-Based Technologies 383 24 Computational Infrastructure and Basic Data Analysis for Next-Generation Sequencing 385 David Sexton 24.1 Introduction 385 24.2 Background 386 24.3 Getting Started with the Next-Generation Manufacturers 387 24.4 Infrastructure and Data Analysis 388 24.5 Applications 392 24.6 Perspectives 392 25 CLC Bio Integrated Platform for Handling and Analysis of Tag Sequencing Data 393 Roald Forsberg, Soren Monsted, and Anne-Mette Hein 25.1 Introduction 393 25.2 Main Components and Features 394 25.3 Applications 396 25.4 Perspectives 404 References 405 26 Multidimensional Context of Sequence Tags: Biological Data Integration 407 Korbinian Grote and Thomas Werner 26.1 Introduction 407 26.2 Methods and Strategies 408 26.3 Perspectives 414 References 415 27 Experimental Design and Quality Control of Next-Generation Sequencing Experiments 417 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 27.1 Introduction 417 27.2 Choice of Platform 417 27.3 Sequencing Depth 420 27.4 Replicates, Randomization, and Statistical Testing 422 27.5 Experimental Controls 425 27.6 General Quality Assessment 427 27.7 Platform-Specific Quality Scores 428 27.8 Quality Checks After Alignment 430 27.9 What Can Go Wrong 431 27.10 Perspectives 432 References 432 28 UTGB Toolkit for Personalized Genome Browsers 435 Taro L. Saito, Jun Yoshimura, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kurosh, and Shinichi Morishita 28.1 Introduction 435 28.2 Overview of the UTGB Toolkit 436 28.3 Methods 438 28.4 Applications 444 28.5 Perspectives 447 References 447 29 Beyond the Pipelines: Cloud Computing Facilitates Management, Distribution, Security, and Analysis of High-Speed Sequencer Data 449 Boris Umylny and Richard S.J. Weisburd 29.1 Introduction 449 29.2 Data Management 450 29.3 Distribution 454 29.4 Analysis 456 29.5 Security 462 29.6 Healthcare Data and Privacy Issues 464 29.7 Sample Evaluation of a Vendor Solution 465 29.8 Perspectives 465 References 467 30 Computational Methods for the Identification of MicroRNAs from Small RNA Sequencing Data 469 Eugene Berezikov 30.1 Introduction 469 30.2 Implementing the miR-Intess Pipeline 470 30.3 Applications 474 References 474 Glossary 477 Link Collection for Next-Generation Sequencing 565 Index 575
