Tag-based Next Generation Sequencing

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.

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, Søren Mønsted, 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

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.