Tag-based Next Generation Sequencing E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1542

Veröffentlichungsjahr: 2011

Beschreibung

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.

Leseprobe

Contents

Cover

Related Titles

Title Page

Copyright

Dedication

Preface

List of Contributors

Part One: Tag-Based Nucleic Acid Analysis

Chapter 1: DeepSuperSAGE: High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies

1.1 Introduction

1.2 Overview of the Protocols

1.3 Methods and Protocols

1.4 Applications

1.5 Perspectives

References

Chapter 2: DeepCAGE: Genome-Wide Mapping of Transcription Start Sites

2.1 Introduction

2.2 What is CAGE?

2.3 Why CAGE?

2.4 Methods and Protocols

2.5 Applications

2.6 Perspectives

References

Chapter 3: Definition of Promotome–Transcriptome Architecture Using CAGEscan

3.1 Introduction

3.2 What is CAGEscan?

3.3 Why CAGEscan?

3.4 Methods and Protocols

3.5 Applications and Perspectives

References

Chapter 4: RACE: New Applications of an Old Method to Connect Exons

4.1 Introduction

4.2 Deep-RACE

4.3 Methods Outline

4.4 Perspectives

References

Chapter 5: RNA-PET: Full-Length Transcript Analysis Using 5'- and 3'-Paired-End Tag Next-Generation Sequencing

5.1 Introduction

5.2 Methods and Protocols

5.3 Applications

5.4 Perspectives

References

Chapter 6: Stranded RNA-Seq: Strand-Specific Shotgun Sequencing of RNA

6.1 Introduction

6.2 Methods and Protocols

6.3 Bioinformatic Considerations

6.4 Applications

6.5 Perspectives

References

Chapter 7: Differential RNA Sequencing (dRNA-Seq): Deep-Sequencing-Based Analysis of Primary Transcriptomes

7.1 Introduction

7.2 What is dRNA-Seq?

7.3 Why dRNA-Seq?

7.4 Methods and Protocols

7.5 Applications

7.6 Perspectives

References

Chapter 8: Identification and Expression Profiling of Small RNA Populations Using High-Throughput Sequencing

8.1 Introduction

8.2 HTS/NGS

8.3 Methods and Protocols

8.4 Troubleshooting

8.5 Applications

8.6 Perspectives

References

Chapter 9: Genome-Wide Mapping of Protein–DNA Interactions by ChIP-Seq

9.1 Introduction

9.2 Methods and Protocols

9.3 Applications

9.4 Perspectives

References

Chapter 10: Analysis of Protein–RNA Interactions with Single-Nucleotide Resolution Using iCLIP and Next-Generation Sequencing

10.1 Introduction

10.2 Procedure Overview

10.3 Antibody and Library Preparation Quality Controls

10.4 Oligonucleotide Design

10.5 Recent Modifications of the iCLIP Protocol

10.6 Troubleshooting

10.7 Methods and Protocols

References

Chapter 11: Massively Parallel Tag Sequencing Unveils the Complexity of Marine Protistan Communities in Oxygen-Depleted Habitats

11.1 Introduction

11.2 Cariaco Basin

11.3 Framvaren Fjord

11.4 Comparison of Cariaco Basin to Framvaren Fjord

11.5 Perspectives on Interpretation of Microbial Eukaryote 454 Data

References

Chapter 12: Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET)

12.1 Introduction

12.2 Methods and Protocols

12.3 Timeline

12.4 Anticipated Results

12.5 Perspectives

References

Chapter 13: Tag-Seq: Next-Generation Tag Sequencing for Gene Expression Profiling

13.1 Introduction

13.2 Protocol Details

13.3 Protocol Overview and Timeline

13.4 Critical Parameters and Troubleshooting

13.5 Methods and Protocols

13.6 Applications

13.7 Perspectives

References

Chapter 14: Isolation of Active Regulatory Elements from Eukaryotic Chromatin Using FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements)

14.1 Introduction

14.2 Methods and Protocols

14.3 Applications

14.4 Perspectives

References

Chapter 15: Identification of Nucleotide Variation in Genomes Using Next-Generation Sequencing

15.1 Introduction

15.2 Methods

15.3 Notes

References

Chapter 16: DGS (Ditag Genome Scanning) – A Restriction-Based Paired-End Sequencing Approach for Genome Structural Analysis

16.1 Introduction

16.2 Methods and Protocols

16.3 Applications

16.4 Perspectives

References

Chapter 17: Next-Generation Sequencing of Bacterial Artificial Chromosome Clones for Next-Generation Physical Mapping

17.1 History of the Bacterial Artificial Chromosome Vector Systems

17.2 History of Physical Mapping

17.3 What is WGP?

17.4 Flow of a WGP Project

17.5 BAC Pooling Strategies

17.6 Methods and Protocols

17.7 Applications

17.8 Perspectives

References

Chapter 18: HELP-Tagging: Tag-Based Genome-Wide Cytosine Methylation Profiling

18.1 Introduction

18.2 Genome-Wide DNA Methylation Analysis

18.3 What is HELP-Tagging?

18.4 Methods and Protocols

18.5 Applications

18.6 Perspectives

References

Chapter 19: Second-Generation Sequencing Library Preparation: In Vitro Tagmentation via Transposome Insertion

19.1 Introduction

19.2 Methods and Protocols

19.3 Perspectives

References

Part Two: Next-Generation Tag-Based Sequencing

Chapter 20: Moving Towards Third-Generation Sequencing Technologies

20.1 Introduction

20.2 Differences Between NGS and Sanger Sequencing

20.3 Preparation of Templates for Sequencing

20.4 Real-Time Sequencing

20.5 Nanopore Sequencing

20.6 Ion Torrent Electronic Sequencing

20.7 Genome Enrichment

20.8 Advantages of NGS

20.9 Problem of Short Reads

20.10 Perspectives

References

Chapter 21: Beyond Tags to Full-Length Transcripts

21.1 Introduction

21.2 Generation of Full-Length Transcriptomes

21.3 Methods

21.4 Applications

21.5 Perspectives

References

Chapter 22: Helicos Single-Molecule Sequencing for Accurate Tag-Based RNA Quantitation

22.1 Introduction

22.2 Methods and Protocols

22.3 Applications

22.4 Perspectives

References

Chapter 23: Total RNA-seq: Complete Analysis of the Transcriptome Using Illumina Sequencing-by-Synthesis Sequencing

23.1 Introduction

23.2 Total RNA-Seq

23.3 Methods and Protocols

23.4 Total RNA-Seq Data Collection and Interpretation

23.5 Applications

References

Part Three: Bioinformatics for Tag-Based Technologies

Chapter 24: Computational Infrastructure and Basic Data Analysis for Next-Generation Sequencing

24.1 Introduction

24.2 Background

24.3 Getting Started with the Next-Generation Manufacturers

24.4 Infrastructure and Data Analysis

24.5 Applications

24.6 Perspectives

Chapter 25: CLC Bio Integrated Platform for Handling and Analysis of Tag Sequencing Data

25.1 Introduction

25.2 Main Components and Features

25.3 Applications

25.4 Perspectives

References

Chapter 26: Multidimensional Context of Sequence Tags: Biological Data Integration

26.1 Introduction

26.2 Methods and Strategies

26.3 Perspectives

References

Chapter 27: Experimental Design and Quality Control of Next-Generation Sequencing Experiments

27.1 Introduction

27.2 Choice of Platform

27.3 Sequencing Depth

27.4 Replicates, Randomization, and Statistical Testing

27.5 Experimental Controls

27.6 General Quality Assessment

27.7 Platform-Specific Quality Scores

27.8 Quality Checks After Alignment

27.9 What Can Go Wrong

27.10 Perspectives

References

Chapter 28: UTGB Toolkit for Personalized Genome Browsers

28.1 Introduction

28.2 Overview of the UTGB Toolkit

28.3 Methods

28.4 Applications

28.5 Perspectives

References

Chapter 29: Beyond the Pipelines: Cloud Computing Facilitates Management, Distribution, Security, and Analysis of High-Speed Sequencer Data

29.1 Introduction

29.3 Distribution

29.4 Analysis

29.5 Security

29.6 Healthcare Data and Privacy Issues

29.7 Sample Evaluation of a Vendor Solution

29.8 Perspectives

References

Chapter 30: Computational Methods for the Identification of MicroRNAs from Small RNA Sequencing Data

30.1 Introduction

30.3 Applications

References

Glossary

Link Collection for Next-Generation Sequencing

Index

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Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or extended by sales representatives or written sales materials. The Advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

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A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http://dnb.d-nb.de.

© 2012 Wiley-VCH Verlag & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley's global Scientific, Technical, and Medical business with Blackwell Publishing.

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Cover Design Formgeber, Eppelheim

Print ISBN: 978-3-527-32819-2

ePDF ISBN: 978-3-527-64477-3

oBook ISBN: 978-3-527-64458-2

ePub ISBN: 978-3-527-64457-5

Mobi ISBN: 3-527-64456-3

We dedicate this book to the memory of late

Eberhard Harbers

who aroused our interest in nucleic acids with one of the first books ever published on this?topic.

Preface

Unprecedented progress in sequencing technologies along with the development of software to interpret the resulting massive DNA sequence data have brought so-called next-generation sequencing technologies into the focus of today's Life Sciences and medical research. Beyond doubt, next-generation sequencing will have a dramatic impact on our understanding of disease and healthcare in the next years to come, and will provide us with entirely new insights into life on Earth.

We know that it is impossible to provide an up-to-date overview on such a rapidly developing field and its future directions within the scope of just one single book. Others have already provided comprehensive overviews on next-generation sequencing technologies and their use in genome sequencing, such as, for example, Michal Janitz with a book entitled Next-Generation Genome Sequencing: Towards Personalized Medicine, also published by Wiley-VCH (2008). Sequencing of entire genomes and resequencing of specific genomic regions such as exons are leading the field at this point, and the results have already started to make rapid changes in biological and medical research.

However, in parallel, many research tools for what is now known as “analytical sequencing” have been designed, and most of them will make next-generation sequencing applications routine for studying biological and medical aspects. At the starting point of “analytical sequencing” the dominant idea was that short sequencing reads – so-called “tags” – could be used for transcript identification. Tag-based approaches were originally designed to increase the throughput of capillary sequencing, where concatemers of such short tag sequences were first used in expression profiling. The new next-generation sequencing platforms largely expanded the use of tag-based approaches, since tag lengths perfectly matched, and still match, the short read lengths of highly parallel sequencing reactions, and therefore avoid concatemerization. Moreover, many of the new applications no longer use restriction endonucleases to limit tag length, which is now determined by the read length into the ends of DNA fragments (also denoted as “sequence census methods”). Today, tag- and sequence census-based approaches cover many applications in genome and transcriptome analysis starting from proteins, DNA, or RNA. Although further progress in next-generation sequencing will yield longer read lengths, tag- and sequence census-based approaches will maintain their important role in Life Sciences, because longer reads are not always required to obtain meaningful data for “analytical sequencing.” Whereas de novo genome sequencing and resequencing will benefit from ever-more powerful sequencing methods, analytical sequencing will shift away from “sequencing power” to better software packages for data analysis and visualization of the resulting immense datasets. It will be essential for common users to make the data more easily accessible and to provide the tools that allow small laboratories without any bioinformatics infrastructure to also work with this kind of data. Moreover, we see a clear need to establish more reference data and better genome annotations, fundamental to data interpretation. In particular, for analytical or diagnostic applications, the success of next-generation sequencing will depend on reliable and reproducible interpretation of the datasets. It is necessary to move away from the descriptive studies at the start of any new technology development towards experiments using replicates and statistical analysis along with trusted references. Today, next-generation sequence data still require powerful bioinformatics that has to be converted into easy-to-use data analysis tools along with a decrease in the cost for running next-generation sequencing experiments. Use of shorter sequencing reads and their reduced information content is one way to reduce experimental cost.

The present book presents an overview of recently developed tag/sequence census-based approaches and current next-generation sequencing technologies, along with an introduction to data analysis. These three topics are reflected in the organization of the book into three major parts. We intentionally excluded chapters on the upcoming third (next-next)-generation sequencer from Pacific Biosciences and Life Technologies' new single-molecule sequencing technology. Although the first instruments of either vendor may already be on the market when this book is published, both methods produce much longer sequence reads (over 1000 bp) not really needed for the methods covered by the present book.

We express our gratitude for the dedicated support and the efforts of all authors working together with us to make this book possible.

September 2011Matthias Harbers Kashiwa (Japan)Günter Kahl Frankfurt am Main (Germany)

List of Contributors

Budrul Ahsan

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex 370

5-1-5 Kashiwanoha

Kashiwa City, Chiba 277-8562

Japan

Artyom A. Alekseyenko

Brigham and Women's Hospital and Harvard Medical School

Division of Genetics

Department of Medicine

77 Avenue Louis Pasteur

Boston, MA 02115

USA

Javier Armisen

Wellcome Trust/Cancer Research UK Gurdon Institute

University of Cambridge

The Henry Wellcome Building of Cancer and Developmental Biology

Tennis Court Road

Cambridge CB2 1QN

UK

Jennifer Asano

University of British Columbia

BC Cancer Agency Genome Sciences Centre

0570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Eugene Berezikov

Hubrecht Institute

Small RNA Biology Research Group

Uppsalalaan 8

3584 CT Utrecht

The Netherlands

Nicolas Bertin

RIKEN Yokohama Institute

Omics Science Center

1-7-22 Suehiro-cho

Tsurumi-ku, Yokohama

Kanagawa 230-0045

Japan

Judith M. Boer

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P P.O. Box 9600

2300 RC Leiden

The Netherlands

and

Erasmus Medical Center

Laboratory of Pediatric Oncology

Erasmus MC-Sophia Children's Hospital room Ee1575, Dr. Molewaterplein 50 3015 GE Rotterdam

The Netherlands

Robert Bogden

Amplicon Express Inc.

2345 NE Hopkins Court

Pullman, WA 99163

USA

Anne Borries

University of Würzburg

Institute for Molecular Infection Biology

Research Center for Infectious Diseases (ZINF)

Josef-Schneider-Straβe 2/Bau D15

97080 Würzburg

Germany

Henk P. Buermans

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

Piero Carninci

RIKEN Yokohama Institute

Omics Science Center

1-7-22 Suehiro-cho

Tsurumi-ku, Yokohama

Kanagawa 230-0045

Japan

Jun Chen

Xiamen University

School of Life Sciences

Department of Ocean Biology

Xiamen, Fujian 361012

China

Allen Delaney

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Johan T. den Dunnen

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

Noreen Dhalla

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Jason Dobry

Amplicon Express Inc.

2345 NE Hopkins Court

Pullman, WA 99163

USA

Mitchell S. Dushay

Illinois Institute of Technology

Division of Biology

Life Sciences Building

3101 South Dearborn Street

Chicago, IL 60616

USA

Virginia Edgcomb

Woods Hole Oceanographic Institution

Department of Geology and Geophysics

266 Woods Hole Road

Woods Hole, MA 02543

USA

Alistair R.R. Forrest

RIKEN Yokohama Institute

Omics Science Center

1-7-22 Suehiro-cho

Tsurumi-ku, Yokohama

Kanagawa 230-0045

Japan

Roald Forsberg

CLC bio

Finlandsgade 10–12

Katrinebjerg

8200 Aarhus N

Denmark

Paul G. Giresi

University of North Carolina at Chapel Hill

Department of Biology and Carolina Center for Genome Sciences

408 Fordham Hall

Chapel Hill, NC 27599-3280

USA

John M. Greally

Albert Einstein College of Medicine

Center for Epigenomics

Department of Genetics

1301 Morris Park Avenue

Bronx, NY 10461

USA

Martien A.M. Groenen

Wageningen University

Animal Breeding and Genomics Center

Marijkeweg 40

6709 PG Wageningen

The Netherlands

Korbinian Grote

Genomatix Software GmbH

Bayerstrasse 85a

80335 Munich

Germany

Matthias Harbers

DNAFORM Inc.

Leading Venture Plaza 2

75-1 Ono-cho

Tsurumi-ku, Yokohama

Kanagawa 230-0046

Japan

Anne-Mette Hein

CLC bio

Finlandsgade 10–12

Katrinebjerg

8200 Aarhus N

Denmark

Matthew S. Hestand

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

and

University of Kentucky

Department of Veterinary Science

Gluck Equine Research Center

1400 Nicholasville Road

Lexington, KY 40546-0099

USA

Martin Hirst

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Joshua W.K. Ho

Brigham and Women's Hospital and Harvard Medical School

Division of Genetics

Department of Medicine

77 Avenue Louis Pasteur

Boston, MA 02115

USA

Stephen Hutchison

454 Life Sciences

15 Commercial Street

Branford, CT 06405

USA

Karolina Janitz

Hawkesbury Institute for the Environment

University of Western Sydney

Hawkesbury Campus, Locked Bag 1797

Penrith, NSW 2751

Australia

Michal Janitz

University of New South Wales

School of Biotechnology and Biomolecular Sciences

Biological Sciences Building

Kensington, NSW 2052

Australia

Thomas Jarvie

454 Life Sciences

15 Commercial Street

Branford, CT 06405

USA

Günter Kahl

University of Frankfurt am Main

Biocenter

Max-von-Lauestraβe 9

60439 Frankfurt am Main

Germany

and

Frankfurt Biotechnology Innovation Center (FIZ)

GenXPro Ltd

Altenhöferallee 3

60438 Frankfurt am Main

Germany

Irina Khrebtukova

Illumina Inc.

Gene Expression Applications

25861 Industrial Boulevard

Hayward, CA 94545

USA

Yeong C. Kim

University of Nebraska Medical Center

Department of Genetics, Cell Biology & Anatomy

42nd and Emile

Omaha, NE 68198

USA

Julian König

MRC Laboratory of Molecular Biology

Division of Structural Studies

Hills Road

Cambridge CB2 0QH

UK

Detlev H. Krüger

Charité – Universitätsmedizin Berlin

Institut für Virologie

Schumannstraβe 20/21

10117 Berlin

Germany

Mitzi I. Kuroda

Brigham and Women's Hospital and Harvard Medical School

Division of Genetics

Department of Medicine

77 Avenue Louis Pasteur

Boston, MA 02115

USA

Reginaldo Kurosh

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex 370

5-1-5 Kashiwanoha

Kashiwa City, Chiba 277-8562

Japan

Yuching Lai

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

Irene Li

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Jason D. Lieb

University of North Carolina at Chapel Hill

Department of Biology and Carolina Center for Genome Sciences

408 Fordham Hall

Chapel Hill, NC 27599-3280

USA

Shujun Luo

Illumina Inc.

Gene Expression Applications

25861 Industrial Boulevard

Hayward, CA 94545

USA

Marco Marra

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Hideo Matsumura

Shinshu University

Gene Research Center

Tokita 3-15-1

Ueda, Nagano 386-8567

Japan

Helen McDonald

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Nicholas J. McGlincy

MRC Laboratory of Molecular Biology

Division of Neurobiology

Hills Road

Cambridge CB2 0QH

UK

Hendrik-Jan Megens

Wageningen University

Animal Breeding and Genomics Center

Marijkeweg 40

6709 PG Wageningen

The Netherlands

Patrice M. Milos

Helicos BioSciences Corporation

One Kendall Square, Building 200

Cambridge, MA 02139

USA

Eric A. Miska

Wellcome Trust/Cancer Research UK Gurdon Institute

University of Cambridge

The Henry Wellcome Building of Cancer and Developmental Biology

Tennis Court Road

Cambridge CB2 1QN

UK

Mohammed Mohiuddin

454 Life Sciences

15 Commercial Street

Branford, CT 06405

USA

Carlos Molina

INRA-URLEG

Unité de Recherche en Légumineuses

17 Rue Sully

21000 Dijon

France

Sren Mnsted

CLC bio

Finlandsgade 10–12

Katrinebjerg

8200 Aarhus N

Denmark

Shinichi Morishita

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex 370

5-1-5 Kashiwanoha

Kashiwa City, Chiba 277-8562

Japan

Sorana Morrissy

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Amy Mraz

Amplicon Express Inc.

2345 NE Hopkins Court

Pullman, WA 99163

USA

Pawan Pandoh

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Peter J. Park

Harvard Medical School

Center for Biomedical Informatics

10 Shattuck Street

Boston, MA 02115

USA

Charles Plessy

RIKEN Yokohama Institute

Omics Science Center

1-7-22 Suehiro-cho

Tsurumi-ku, Yokohama

Kanagawa 230-0045

Japan

Anna-Liisa Prabhu

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Marcel Prins

KeyGene NV

6700 AE Wageningen

The Netherlands

Tal Raz

Helicos BioSciences Corporation

One Kendall Square, Building 700

Cambridge, MA 02139

USA

Xiaoan Ruan

Genome Institute of Singapore

Genome Technology and Biology

60 Biopolis Street

#02-01 Genome

Singapore

Singapore

Yijun Ruan

Genome Institute of Singapore

Genome Technology and Biology

60 Biopolis Street

#02-01 Genome

Singapore 138672

Singapore

Taro L. Saito

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex

5-1-5 Kashiwanoha

Kashiwa City, Chiba

Japan

Atsushi Sasaki

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex 370

5-1-5 Kashiwanoha

Kashiwa City, Chiba 277-8562

Japan

Gary P. Schroth

Illumina Inc.

Gene Expression Applications

25861 Industrial Boulevard

Hayward, CA 94545

USA

David Sexton

Baylor Medical College Human Genome

Sequencing Center

2005 South Mason Rd #906

Katy, TX 77450

USA

Cynthia M. Sharma

University of Würzburg

Institute for Molecular Infection Biology

Research Center for Infectious Diseases (ZINF)

Josef-Schneider-Straβe 2/Bau D15

97080 Würzburg

Germany

W. Robert Shaw

Imperial College London

Department of Life Sciences

London SW7 2AZ

UK

Geoffrey P. Smith

Illumina Cambridge Ltd.

Sequencing Research

Little Chesterford

Essex CB10 1XL

UK

Thorsten Stoeck

University of Kaiserslautern

Faculty of Biology

Ecology Department

Erwin-Schrödinger Straβe 14

67663 Kaiserslautern

Germany

Keith Stormo

Amplicon Express Inc.

2345 NE Hopkins Court

Pullman, WA 99163

USA

Masako Suzuki

Albert Einstein College of Medicine

Center for Epigenomics

Department of Genetics

1301 Morris Park Avenue

Bronx, NY 10461

USA

Fraz Syed

Epicentre Biotechnologies

726 Post Road

Madison, WI 53713

USA

Angela Tam

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Quanzhou Tao

Amplicon Express Inc.

2345 NE Hopkins Court

Pullman, WA 99163

USA

Ryohei Terauchi

Iwate Biotechnology Research Center

Research Group of Genetics and Genomics

Narita 22-174-4

Kitakami, Iwate 024-0003

Japan

Peter A.C. 't Hoen

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

and

Leiden University Medical Center

Leiden Genome Technology Center

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

John F. Thompson

Helicos BioSciences Corporation

One Kendall Square, Building 700

Cambridge, MA 02139

USA

Jernej Ule

MRC Laboratory of Molecular Biology

Division of Structural Studies

Hills Road

Cambridge CB2 0QH

UK

Boris Umylny

Japan Bioinformatics KK

Yoyogiekimae Building 401

1-36-6 Yoyogi, Shibuya-ku

Tokyo 151-0053

Japan

Michiel van Eijk

KeyGene NV

6700 AE Wageningen

The Netherlands

Michiel van Galen

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

Mark van Haaren

KeyGene NV

6700 AE Wageningen

The Netherlands

Maarten van Iterson

Leiden University Medical Center

Center for Human and Clinical Genetics

Postal Zone S4-P

P.O. Box 9600

2300 RC Leiden

The Netherlands

Jan van Oeveren

KeyGene NV

6700 AE Wageningen

The Netherlands

Jörg Vogel

University of Würzburg

Institute for Molecular Infection Biology

Research Center for Infectious Diseases (ZINF)

Josef-Schneider-Straβe 2/Bau D15

97080 Würzburg

Germany

San Ming Wang

University of Nebraska Medical Center

Department of Genetics, Cell Biology & Anatomy

42nd and Emile

Omaha, NE 68198

USA

Richard S.J. Weisburd

ELSS Inc.

2504-3 Saiki

Tsukuba

Ibaraki 305-0028

Japan

Thomas Werner

Genomatix Software GmbH

Bayerstrasse 85a

80335 Munich

Germany

Jon Wittendorp

KeyGene NV

6700 AE Wageningen

The Netherlands

Jun Yoshimura

University of Tokyo

Graduate School of Frontier Sciences

Department of Computational Biology

Kashiwa Research Complex 370

5-1-5 Kashiwanoha

Kashiwa City, Chiba 277-8562

Japan

Yongjun Zhao

University of British Columbia

BC Cancer Agency Genome Sciences Centre

570 West 7th Avenue

Vancouver, BC V5Z 4S6

Canada

Part One

Tag-Based Nucleic Acid Analysis

Chapter 1

DeepSuperSAGE: High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies

Hideo Matsumura, Carlos Molina, Detlev H. Krüger, Ryohei Terauchi, and Günter Kahl

Abstract

SuperSAGE is a variant of the serial analysis of gene expression (SAGE) expression profiling technology, in which 26-bp tags are extracted from cDNA using the type III restriction endonuclease EcoP15I. The use of a longer tag size in SuperSAGE allows a secure tag-to-gene annotation by homology searches against genome, transcript, or expressed sequence tag sequences. For organisms without genomic information, the 26-bp tags can be used as polymerase chain reaction primers to recover the full-length cDNA by 5′- and 3′-rapid amplification of cDNA ends. Here, we present the combination of SuperSAGE and high-throughput sequencing technologies (now- or next-generation sequencing (NGS)). We coin this merger deepSuperSAGE. The direct sequencing of millions of tag fragments shortens time and reduces costs for the analysis enormously. Furthermore, the incorporation of an indexing system expands the potential of deepSuperSAGE to analyze multiple samples in a single NGS run. The most recent version of deepSuperSAGE (high-throughput SuperSAGE) at least equals or even outcompetes microarrays in throughput. These improvements allow the application of deepSuperSAGE in transcriptome analysis in any eukaryotic system.