Cefalometría. Descripción y Aplicaciones
60.18 €
63.35 €
Felgueroso
Whatsapp
[+34] 630 929 946
0
0,00
€
Tag-based Next Generation Sequencing
195 €
185.25 €
Reseña o resumen
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, S ren M nsted, 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
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, S ren M nsted, 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
Ficha del libro
ISBN
978-3-527-32819-2
EAN
9783527328192
Editor
John Wiley & Sons, Ltd.
Stock
NO
Idioma
Inglés
Nivel
Profesional
Formato
Encuadernado
Tapa Dura
Páginas
608
Largo
-
Ancho
-
Peso
-
Edición
Fecha de edición
15-12-2011
Año de edición
2011
Nº de ediciones
1
Colección
-
Nº de colección
-
