Sound insulation in buildings:
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| Format: | Electronic eBook |
| Language: | English |
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Boca Raton
CRC Press, Taylor & Francis Group
[2018]
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| Online Access: | DE-573 DE-91 Volltext Inhaltsverzeichnis |
| Physical Description: | 1 Online-Ressource (xxv, 450 Seiten) |
| ISBN: | 9781498700429 9781351230728 9781351228206 |
| DOI: | 10.1201/9781351228206 |
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IMAGE 1
VIL
CONTENTS
PREFACE XIX LIST OF CONTRIBUTORS XXI
PART ONE TAG-BASED NUCLEIC ACID ANALYSIS 7
1 DEEPSUPERSACE: HIGH-THROUGHPUT TRANSCRIPTOME SEQUENCING WITH NOW- AND
NEXT-GENERATION SEQUENCING TECHNOLOGIES 3 HIDEO MATSUMURA, CARLOS
MOLINA, DETLEV H. KRUEGER, RYOHEI TERAUCHI, AND GUENTER KAHL 1.1
INTRODUCTION 3
1.2 OVERVIEW OF THE PROTOCOLS 5 1.2.1 PRINCIPLE OF THE SUPERS AGE METHOD
5 1.2.2 POWER OF THE SUPERSAGE TAG 5 1.2.3 DEVELOPMENT OF DEEPSUPERSAGE
6
1.2.4 DITAG-BASED DEEPSUPERSAGE (FOR 454 PYROSEQUENCING) 7 1.2.5
SINGLE-TAG-BASED DEEPSUPERSAGE (HT-SUPERSAGE) 8 1.3 METHODS AND
PROTOCOLS 9
1.3.1 LINKER OR ADAPTER PREPARATION 9 1.3.2 RNA SAMPLES 10 1.3.3 CDNA
SYNTHESIS AND NLALLL DIGESTION 10
1.3.4 TAG EXTRACTION FROM CDNA 10 1.3.5 TAG EXTRACTION FROM CDNA 11
1.3.6 PURIFICATION OF LINKER-TAG FRAGMENTS 12 1.3.7 DITAG OR ADAPTER-TAG
FORMATION AND AMPLIFICATION 12 1.3.8 PREPARATION OF TEMPLATES FOR
SEQUENCING 14 1.4 APPLICATIONS 14
1.4.1 APPLICATIONS OF DEEPSUPERSAGE IN COMBINATION WITH 454
PYROSEQUENCING 14 1.4.2 PRACTICAL ANALYSIS OF HT-SUPERSAGE 18 1.5
PERSPECTIVES 19
REFERENCES 20
2 DEEPCACE: GENOME-WIDE MAPPING OF TRANSCRIPTION START SITES 23 MATTHIAS
HARBERS, MITCHELL S. DUSHAY, AND PIERO CAMINA 2.1 INTRODUCTION 23
2.2 WHAT IS CAGE? 24
2.3 WHY CAGE? 26
2.4 METHODS AND PROTOCOLS 28 2A.I KEY REAGENTS AND CONSUMABLES 28 2.4.2
PRECAUTIONS 30
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/1011200392
DIGITALISIERT DURCH
IMAGE 2
VIII CONTENTS
2.4.3 RNA SAMPLES USED FOR DEEPCAGE LIBRARY PREPARATION 30 2.4.4
DEEPCAGE LIBRARY PREPARATION 32 2.5 APPLICATIONS 43
2.6 PERSPECTIVES 44
REFERENCES 45
3 DEFINITION OFPROMOTOME-TRANSCRIPTOME ARCHITECTURE USING CACESCAN 47
NICOLAS BERTIN, CHARLES PLESSY, PIERO CAMINA, AND MATTHIAS HARBERS
3.1 INTRODUCTION 47
3.2 WHAT IS CAGESCAN? 48
3.3 WHY CAGESCAN? 50
3.4 METHODS AND PROTOCOLS 51
3.4.1 KEY REAGENTS AND CONSUMABLES 51 3.4.2 PRECAUTIONS 53
3.4.3 RNA SAMPLES USED FOR CAGESCAN LIBRARY PREPARATION 53 3.4.4
CONSIDERATIONS ON POOLING CAGESCAN LIBRARIES 54 3.4.5 CAGESCAN LIBRARY
PREPARATION 54 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
4.2.1 CHOICE OF THE SEQUENCER 65 4.2.2 VALIDATION OF PROMOTER STUDIES 65
4.2.3 OTHER APPLICATIONS OF DEEP-RACE 66 4.2.4 LIMITATIONS OF DEEP-RACE
66
4.3 METHODS OUTLINE 67
4.3.1 PRIMER DESIGN 67
4.3.2 MOLECULAR BIOLOGY OF DEEP-RACE LIBRARY PREPARATION 67 4.3.3
SEQUENCING OF DEEP-RACE LIBRARIES 68 4.3.4 ANALYSIS 68
4.4 PERSPECTIVES 70
REFERENCES 71
5 RNA-PET: FULL-LENGTH TRANSCRIPT ANALYSIS USING 5'- AND 3'-PAIRED-END
TAG NEXT-GENERATION SEQUENCING 73 XIAOAN RUAN AND YIJUN RUAN 5.1
INTRODUCTION 73
5.2 METHODS AND PROTOCOLS 75
5.2.1 KEY REAGENTS AND CONSUMABLES 75 5.2.2 PROTOCOL 78
5.3 APPLICATIONS 88
5.3.1 PET SEQUENCING WITH SOIID 88 5.3.2 MAPPING OF THE PETS 88 5.3.3
PET CLUSTERING, ANNOTATION, AND GENOME BROWSER VISUALIZATION 89 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
6.1.1 BEFORE STARTING 93 6.2 METHODS AND PROTOCOLS 93
6.2.1 PREFACE 93
6.2.2 MATERIALS AND CONSUMABLES 94
IMAGE 3
CONTENTS IX
6.2.3 PROTOCOL 95
6.3 BIOINFORMARIC 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 709 ANNE BORRIES, JOERG VOGEL, AND CYNTHIA M.
SHARMA 7.1 INTRODUCTION 109
7.2 WHAT IS DRNA-SEQ? ILL
7.3 WHY DRNA-SEQ? 112 7.4 METHODS AND PROTOCOLS 115 7 A.I MATERIALS AND
CONSUMABLES 115 7.4.2 PRECAUTIONS 116 7.4.3 RNA SAMPLES USED FOR
DRNA-SEQ LIBRARY PREPARATION 116 7.4.4 DRNA-SEQ LIBRARY PREPARATION 116
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
8.1.1 MIRNAS 123 8.1.2 PIRNAS 125
8.1.3 SIRNAS 126
8.1.4 OTHER SMALL RNAS 126 8.2 HTS/NGS 127
8.3 METHODS AND PROTOCOLS 128 8.3.1 KEY REAGENTS AND SOLUTIONS 128 8.3.2
TOTAL RNA ISOLATION 129 8.3.3 SMALL RNA ISOLATION 129 8.3.4 LIGATION OF
ADAPTERS 131 8.4 TROUBLESHOOTING 134 8.5 APPLICATIONS 134
8.6 PERSPECTIVES 136
REFERENCES 138
9 GENOME-WIDE MAPPING OF PROTEIN-DNA INTERACTIONS BY CHLP-SEQ 739 JOSHUA
W.K. HO, ARTYOM A. ALEKSEYENKO, MITZI I. KURODA, AND PETERJ. PARK 9.1
INTRODUCTION 139
9.2 METHODS AND PROTOCOLS 141 9.2.1 ANTIBODY VALIDATION 141 9.2.2 CHIP
141
9.2.3 SEQUENCING LIBRARY PREPARATION 144 9.2.4 DATA ANALYSIS 146 9.3
APPLICATIONS 147
9.3.1 DECIPHERING THE TRANSCRIPTIONAL REGULATORY PROGRAM 148 9.3.2
UNRAVELING EPIGENETIC REGULATION 148 9.3.3 COMPARATIVE INTERINDIVIDUAL
OR INTERSPECIES ANALYSIS 149 9.3.4 STUDY OF HUMAN DISEASES AND CLINICAL
APPLICATIONS 149 9.3.5 ADVANTAGES AND CHALLENGES OF CHLP-SEQ 149 9.4
PERSPECTIVES 150
REFERENCES 151
IMAGE 4
CONTENTS
10 ANALYSIS OF PROTEIN-RNA INTERACTIONS WITH SINGLE-NUCLEOTIDE
RESOLUTION USING CLIP AND NEXT-GENERATION SEQUENCING 153 JULIAN KOENIG,
NICHOLAS J. MCCLINCY, ANDJERNEJ 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 OFTHEICLIP 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 777 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
(CHLA-PET) 185 XIAOAN RUAN AND YIJUN RUAN 12.1 INTRODUCTION 185 12.1.1
DEVELOPMENT OF THE CHI A-PET METHOD 186 12.1.2 APPLICATIONS OF THE
CHLA-PET METHOD 187 12.1.3 EXPERIMENTAL DESIGN OF CHLA-PET ANALYSIS 187
12.1.3.1 CHIP SAMPLE PREPARATION 187 12.1.3.2 CHLA-PET LIBRARY
CONSTRUCTION 189 12.1.3.3 CHLA-PET LIBRARY SEQUENCING AND MAPPING 190
12.1.3.4 CONTROL LIBRARIES 191
12.2 METHODS AND PROTOCOLS 192 12.2.1 KEY REAGENTS AND CONSUMABLES 192
12.2.2 PROTOCOL 195 12.3 TIMELINE 206 12.4 ANTICIPATED RESULTS 207
12.4.1 VERIFICATION OF SONICATED CHROMATIN DNA SIZE RANGE 207 12.4.2
CHIP QUALITY CONTROL: YIELD AND ENRICHMENT 207 12.4.3 CHLA-PET LIBRARY
QUALITY CONTROL 207
12 A A CHI A-PET SEQUENCING AND MAPPING ANALYSIS 207 12.5 PERSPECTIVES
209 REFERENCES 209
13 TAG-SEQ: NEXT-GENERATION TAG SEQUENCING FOR GENE EXPRESSION PROFILING
277
SORANA MORRISSY, YONGJUN ZHAO, ALLEN DELANEY, JENNIFER ASANO, NOREEN
DHALLA, IRENE LI, HELEN MCDONALD, PAWAN PANDOH, ANNA-LIISA PRABHU,
ANGELA TARN, MARTIN HIRST, AND MARCO MARRA
13.1 INTRODUCTION 232 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 13.5.1 BASIC PROTOCOL 1: FIRST- AND
SECOND-STRAND CDNA SYNTHESIS FOR TAG-SEQ LIBRARY CONSTRUCTION 215
IMAGE 5
CONTENTS XI
13.5.2 BASIC PROTOCOL 2: TAG GENERATION 219 13.5.3 BASIC PROTOCOL 3: PCR
AND FRAGMENT ISOLATION 223 13.5.4 BASIC PROTOCOL 4: PREPARING THE
LIBRARY FOR ILLUMINA SEQUENCING 226 13.5.5 ALTERNATE PROTOCOL: AMPLIFIED
TAG-SEQ LIBRARY CONSTRUCTION
(TAG-SEQLITE) 227
13.5.6 BASIC PROTOCOL 5: DATA ANALYSIS 232 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 C. CIRESI AND JASON D. LIEB
14.1 INTRODUCTION 243
14.2 METHODS AND PROTOCOLS 245 14.2.1 FAIRE PROCEDURE 245 14.2.2
OPTIMIZATION OF THE FAIRE PROCEDURE 245 14.2.3 EQUIPMENT AND REAGENTS
246 14.2.4 DETECTION OF FAIRE DNA 250 14.2.5 HIGH-THROUGHPUT SEQUENCING
252 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
15.1.1 SNP DISCOVERY AND NUCLEOTIDE VARIATION ASSESSMENT 259 15.1.2
SEQUENCE AND LIBRARY PREPARATION STRATEGIES 259 15.2 METHODS 261
15.2.1 PREPROCESSING OF READS 262 15.2.1.1 FASTQ FORMAT 262 15.2.1.2
FASTQ FORMAT - ILLUMINA VERSION 262 15.2.1.3 ILLUMINA FASTQ TO SAENGER
FASTQ 263 15.2.1.4 ABI SOIID- AND ROCHE 454-SPECIFIC FORMATS 264
15.2.1.5 ILLUMINA SCARF OR QSEQ TO FASTQ 264 15.2.1.6 QUALITY EVALUATION
265 15.2.1.7 HANDLING ADAPTER SEQUENCES - LINKERS AND BARCODES 265
15.2.1.8 QUALITY TRIMMING 266 15.2.2 MAPPING READS TO A REFERENCE GENOME
266 15.2.2.1 MAKING ALIGNMENTS USING MOSAIK 267 15.2.2.2 MAKING
ALIGNMENTS USING BWA 268 15.2.3 VARIANT CALLING 269 15.2.3.1 SAM FORMAT
270
15.2.3.2 VARIANT CALLING WITH SAMTOOLS 273 15.2.3.3 VARIANT CALLING WITH
GATK 274 15.3 NOTES 275
REFERENCES 275
16 DCS (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 16.2.1 CLONING-BASED DGS PROTOCOL 278
16.2.2 NON-CLONING-BASED DGS PROTOCOL 281
IMAGE 6
XII
CONTENTS
16.2.3 16.3 16.3.1 16.3.2 16.3.3 16.4
17
17.1 17.2 17.3 17.4 17.5 17.6 17.6.1 17.6.2 17.6.3 17.6.4 17.6.5 17.7
17.7.1 17.7.2 17.7.3 17.8
18.1 18.2 18.3 18.3.1 18.4 18.4.1 18.4.2 18.4.3 18.4.4 18.4.5 18.4.6
18.5 18.6
19
19.1 19.2 19.2.1 19.2.2 19.3
COMPUTATIONAL MAPPING ANALYSIS OF EXPERIMENTAL DITAGS 282 APPLICATIONS
283 ANALYZING NORMAL GENOME STRUCTURE 283 IDENTIFYING SOMATIC
REARRANGEMENTS IN CANCER GENOMES 283 A USEFUL TOOL TO STUDY FAMILY
GERMLINE GENETIC DISORDERS 284
PERSPECTIVES 284 REFERENCES 285
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 PRINSJON WITTENDORP, AND MARK
VAN HAAREN HISTORY OF THE BACTERIAL ARTIFICIAL CHROMOSOME VECTOR SYSTEMS
287
HISTORY OF PHYSICAL MAPPING 288 WHAT IS WGP? 289 FLOW OF A WGP PROJECT
289 BAC POOLING STRATEGIES 290 METHODS AND PROTOCOLS 291 BAC LIBRARY AND
POOLING STRATEGY 291 SAMPLE PREPARATION FOR ILLUMINA SEQUENCING 292
ILLUMINA SEQUENCING 293 DECONVOLUTION TO ASSIGN THE BAC ADDRESS TO EACH
READ 293 CONTIG BUILDING 293
APPLICATIONS 294 RESULTS FROM REAL WGP PROJECTS PERFORMED BY THE AUTHORS
294 REORGANIZING PROJECT FUNDING AND SEQUENCING BUDGETS 295 UNLEASH THE
POWER OF BAC CLONES 296
PERSPECTIVES 296 REFERENCES 297
HELP-TAGGING: TAG-BASED GENOME-WIDE CYTOSINE METHYLATION PROFILING 299
MASAKO SUZUKI AND JOHN M. GREATLY INTRODUCTION 299 GENOME-WIDE DNA
METHYLATION ANALYSIS 299 WHAT IS HELP-TAGGING? 300 WHEN IS HELP-TAGGING
THE PREFERRED CYTOSINE METHYLATION ASSAY?
METHODS AND PROTOCOLS 301 REAGENTS, MATERIALS, AND EQUIPMENT 301 BUFFERS
AND ADAPTERS FOR HELP-TAGGING LIBRARY PREPARATION 302 PRECAUTIONS 303
DNA SAMPLES FOR HELP-TAGGING LIBRARY PREPARATION 303 HELP-TAGGING
LIBRARY PREPARATION 304 ILLUMINA SEQUENCING 307
APPLICATIONS 308 PERSPECTIVES 308 REFERENCES 309
301
SECOND-GENERATION SEQUENCING LIBRARY PREPARATION: IN VITRO TAGMENTATION
VIA TRANSPOSOME INSERTION 577 FRAZ SYED INTRODUCTION 311
METHODS AND PROTOCOLS 313 MATERIALS 313 METHODS 314
PERSPECTIVES 321 REFERENCES 321
IMAGE 7
CONTENTS | XIII
PART TWO NEXT-GENERATION TAG-BASED SEQUENCING 323
20 MOVING TOWARDS THIRD-GENERATION SEQUENCING TECHNOLOGIES 325 KAROLINA
JANITZ AND MICHALJANITZ 20.1 INTRODUCTION 325
20.2 DIFFERENCES BETWEEN NGS AND SAENGER SEQUENCING 326 20.3 PREPARATION
OF TEMPLATES FOR SEQUENCING 326 20.3.1 NEXT GENERATION: SINGLE-MOLECULE
TEMPLATES 327 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 21.2.1 MRNA
FRAGMENTATION AND PREPARATION FOR SEQUENCING 339 21.2.1.1 STEP 1: MRNA
PREPARATION 339 21.2.1.2 STEP 2: FRAGMENTATION 339 21.2.1.3 STEP 3:
FIRST-STRAND SYNTHESIS 340
21.2.1.4 STEP 4: SECOND-STRAND SYNTHESIS AND LIBRARY PREPARATION 340
21.2.2 SEQUENCING OF FULL-LENGTH TRANSCRIPTOMES 341 21.3 METHODS 342
21.3.1 ASSEMBLY 342 21.3.2 MAPPING 343 21A APPLICATIONS 344
21.4.1 MODEL ORGANISMS 344 21.4.2 FUSION TRANSCRIPT DETECTION 347 21.4.3
DIGITAL GENE EXPRESSION 349 21.4.4 ALLELE-SPECIFIC EXPRESSION 349 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 22.2.1 REAGENTS, REQUIRED PRIMERS, AND
THERMOCYDER PROGRAMS 355 22.2.2 STANDARD PRECAUTIONS 357 22.2.3 DGE
SAMPLE PREPARATION 357
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*3.1 KEY
MATERIALS 369
IMAGE 8
XIV
CONTENTS
23.3.2 METHOD 370
23.4 TOTAL RNA-SEQ DATA COLLECTION AND INTERPRETATION 23.5 APPLICATIONS
380
REFERENCES 381
378
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 24.4.1 COMPUTATIONAL CONSIDERATIONS
388 24.4.2 DATA DYNAMICS 389
24.4.3 SOFTWARE AND POSTANALYSIS 390 24.4.4 STAFFING REQUIREMENTS 391
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 M0NSTED, AND ANNE-METTE HEIN
25.1 INTRODUCTION 393
25.2 MAIN COMPONENTS AND FEATURES 394 25.2.1 DATA FLOW AND DATA BACK-END
394 25.2.2 CLC GENOMICS WORKBENCH 394 25.2.3 CLC GENOMICS SERVER 395
25.2.4 APIS 396
25.2.5 ACCELERATION OF ANALYSIS 396 25.3 APPLICATIONS 396
25.3.1 FIRST-LEVEL ANALYSIS 396 25.3.1.1 IMPORT 396 25.3.1.2
DEMULTIPLEXING 397 25.3.1.3 TRIM AND QUALITY CONTROL 397 25.3.2 SECOND
AND THIRD LEVELS - APPLICATION-SPECIFIC STEPS 398 25.3.2.1 RNA-SEQ 398
25.3.2.2 SMALLRNA-SEQ 399 25.3.2.3 TAG-SEQ 400 25.3.2.4 CHLP-SEQ 401
25.3.3 FOURTH LEVEL - EXPRESSION ANALYSIS 403 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 26.2.1 ANNOTATION LINKS SEQUENCE TAGS
(READS) TO BIOLOGY 408 26.2.2 APPLICATION OF THE METHODS AND STRATEGIES
410 26.2.3 ONLY POSITIVE RESULTS ARE CONCLUSIVE 411 26.2 A AUTOMATIC
WORKFLOW: CHLP-SEQ OF PEROXISOME PROLIFERATOR-ACTIVATED
RECEPTOR-Y 412
26.3 PERSPECTIVES 414
REFERENCES 415
IMAGE 9
CONTENTS XV
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,
ANDJOHAN T. DEN DUENNEN 21. 1 INTRODUCTION 417
27.2 CHOICE OF PLATFORM 417
27.2.1 READ LENGTH AND NUMBER OF READS 418 27.2.2 SINGLE-END VERSUS
PAIRED-END SEQUENCING 419 27.2.3 PLATFORM-SPECIFIC ADVANTAGES AND
DISADVANTAGES 419 27.3 SEQUENCING DEPTH 420 27.3.1 EXPRESSION PROFILING
420 27.3.2 CHLP-SEQ: RELATION ENRICHMENT FACTOR AND SEQUENCING DEPTH 421
27.3.3 BARCODING 422 27 A REPLICATES, RANDOMIZATION, AND STATISTICAL
TESTING 422 27'.4.1 TECHNICAL AND BIOLOGICAL REPLICATES 422 27.4.2
TECHNICAL VARIABILITY 423 27 A3 BIOLOGICAL REPLICATES INCREASE ACCURACY
424 27'A4 SAMPLE SIZE 424 27.4.5 IMPORTANCE OF RANDOMIZING SAMPLES 424
27.5 EXPERIMENTAL CONTROLS 425 27.5.1 SPIKE-INS 425 27.5.2 NEGATIVE
CONTROLS IN CHLP-SEQ EXPERIMENTS 426 27.6 GENERAL QUALITY ASSESSMENT 427
27.6.1 NUCLEOTIDE FREQUENCY CHARACTERISTICS 428 27.6.2 PERCENTAGE
DUPLICATE READS 428 27.7 PLATFORM-SPECIFIC QUALITY SCORES 428 27.7.1
SANGER, ROCHE, ILLUMINA, AND SOLID QUALITY SCORES 429 27.7.2 CONVERSION
AND VISUALIZATION OF QUALITY SCORES 429 27.8 QUALITY CHECKS AFTER
ALIGNMENT 430 27.8.1 PERCENTAGE OF READS ALIGNED AND PERCENTAGE IN
REPEAT REGIONS 430 27.8.2 DEEPSAGE: PERCENTAGE 21-22MERS 430 27.8.3
RNA-SEQ: PERCENTAGE TAGS IN ANNOTATED TRANSCRIPTS 430 21.SA MIRNA
PROFILING: PERCENTAGE IN ANNOTATED MIRNAS 450 27.8.5 CHLP-SEQ:
ENRICHMENT 430 27.8.6 CORRELATION MEASURES 431 27.9 WHAT CAN GO WRONG
431
27.9.1 SAMPLE SWAPS 431 27.9.2 CONTAMINATION 431 27.10 PERSPECTIVES 432
REFERENCES 432
28 UTGB TOOLKIT FOR PERSONALIZED GENOME BROWSERS 435 TARO L. SAITOJUN
YOSHIMURA, BUDRUL AHSAN, ATSUSHI SASAKI, REGINALDO KUROSH, AND SHINICHI
MORISHITA 28.1 INTRODUCTION 435
28.2 OVERVIEW OF THE UTGB TOOLKIT 436 28.2.1 AVAILABILITY OF THE UTGB
TOOLKIT 438 28.3 METHODS 438
28.3.1 INSTALLATION OF THE UTGB TOOLKIT 438 28.3.1.1 PREREQUISITES 438
28.3.1.2 EASY INSTALLER 438 28.3.1.3 MAC OS X AND LINUX 438
28.3.1.4 WINDOWS 439 28.3.2 RUNNING THE UTGB TOOLKIT 439 28.3.3 VIEWING
HELP MESSAGES 439 28.3.4 CREATING A NEW UTGB PROJECT 440
IMAGE 10
XVI CONTENTS
28.3.5 BUILDING A GENOME BROWSER 441 28.3.6 LAUNCHING A PORTABLE WEB
SERVER 441 28.3.7 CONFIGURING TRACK VIEWS 441 28.3.8 ADDING A NEW TRACK
442 28.3.8.1 FASTATRACK 442 28.3.8.2 READTRACK 442
28.3.8.3 WIGTRACK 443 28.3.8.4 ADDING KEYWORD SEARCH 443 28.3.9
SWITCHING VIEWS 443 28.3.10 PUBLISHING YOUR GENOME BROWSER 443 28.3.11
MANUAL INSTALLATION OF UTGB TOOLKIT (OPTIONAL) 444 28.3.11.1 WINDOWS 444
28.3.11.2 MAC OS X AND LINUX 444 28.3.12 DEVELOPING YOUR OWN TRACKS 444
28.4 APPLICATIONS 444
28.4.1 PORTABLE WEB SERVER FOR QUICKLY BROWSING LOCAL RESOURCES 444
28.4.2 PORTABLE DATABASE ENGINE 445 28.4.3 WEB APPLICATION DEVELOPMENT
FRAMEWORK 446
28.4.3.1 SERVER-SIDE PROGRAMMING SUPPORT 446 28.4.3.2 WEB ACTION 446
28.4.3.3 DATABASE CONNECTION 446 28.4.3.4 OBJECT-DATABASE MAPPING 446
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
29.2.1 DATA QUANTITY 450 29.2.2 HSSS 451
29.2.3 DATA ANALYSIS 452 29.2.4 DATA SIZE 453
29.3 DISTRIBUTION 454
29.3.1 COLLABORATION 454 29.3.2 DISTRIBUTION OF DATA, ANNOTATIONS, AND
ANALYSIS TOOLS 455 29.4 ANALYSIS 456
29A.I INTEGRATING DATA REPOSITORIES AND ANALYTICS 456 29.4.2 INTEGRATING
HSS DISCOVERY PIPELINES WITH ANNOTATION DATA 458 29.4.3 INTEGRATING HSS
AND TRADITIONAL ANALYSIS ALGORITHMS 459 29AA CLOUD-BASED INFRASTRUCTURE
461 29.5 SECURITY 462
29.6 HEALTHCARE DATA AND PRIVACY ISSUES 464 29 '.1 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 30.2.1 PREPROCESSING OF
SMALL RNA SEQUENCING DATA 470 30.2.2 MAPPING OF SMALL RNA READS TO THE
GENOME 471 30.2.3 ANNOTATION 471 30.2.4 IDENTIFICATION OF HAIRPIN
STRUCTURES 472
IMAGE 11
CONTENTS XVII
30.2.5 MIRNA SIGNATURES 472 30.2.6 MIRNA EXPRESSION PROFILES 474 30.3
APPLICATIONS 474
REFERENCES 474
GLOSSARY 477
LINK COLLECTION FOR NEXT-GENERATION SEQUENCING 565
INDEX 575 |
| any_adam_object | 1 |
| author | Rindel, Jens Holger |
| author_GND | (DE-588)1081184000 |
| author_facet | Rindel, Jens Holger |
| author_role | aut |
| author_sort | Rindel, Jens Holger |
| author_variant | j h r jh jhr |
| building | Verbundindex |
| bvnumber | BV044990020 |
| collection | ZDB-30-PQE ZDB-7-TFC |
| ctrlnum | (ZDB-30-PQE)EBC4912142 (ZDB-89-EBL)EBL4912142 (ZDB-38-EBR)ebr11462760 (OCoLC)1011200392 (DE-599)BVBBV044990020 |
| dewey-full | 693.834 |
| dewey-hundreds | 600 - Technology (Applied sciences) |
| dewey-ones | 693 - Specific materials & purposes |
| dewey-raw | 693.834 |
| dewey-search | 693.834 |
| dewey-sort | 3693.834 |
| dewey-tens | 690 - Construction of buildings |
| discipline | Bauingenieurwesen |
| doi_str_mv | 10.1201/9781351228206 |
| format | Electronic eBook |
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| id | DE-604.BV044990020 |
| illustrated | Not Illustrated |
| indexdate | 2024-10-11T10:00:42Z |
| institution | BVB |
| isbn | 9781498700429 9781351230728 9781351228206 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030382268 |
| oclc_num | 1011200392 |
| open_access_boolean | |
| owner | DE-91 DE-BY-TUM DE-573 |
| owner_facet | DE-91 DE-BY-TUM DE-573 |
| physical | 1 Online-Ressource (xxv, 450 Seiten) |
| psigel | ZDB-30-PQE ZDB-7-TFC ZDB-30-PQE TUM_PDA_PQE_Kauf |
| publishDate | 2018 |
| publishDateSearch | 2018 |
| publishDateSort | 2018 |
| publisher | CRC Press, Taylor & Francis Group |
| record_format | marc |
| spelling | Rindel, Jens Holger Verfasser (DE-588)1081184000 aut Sound insulation in buildings Jens Holger Rindel Boca Raton CRC Press, Taylor & Francis Group [2018] 1 Online-Ressource (xxv, 450 Seiten) txt rdacontent c rdamedia cr rdacarrier Soundproofing Schalldämmung (DE-588)4052023-7 gnd rswk-swf Gebäude (DE-588)4156127-2 gnd rswk-swf Schalldämmung (DE-588)4052023-7 s Gebäude (DE-588)4156127-2 s DE-604 Erscheint auch als Druck-Ausgabe 978-1-4987-0041-2 https://doi.org/10.1201/9781351228206 Verlag URL des Erstveröffentlichers Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030382268&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Rindel, Jens Holger Sound insulation in buildings Soundproofing Schalldämmung (DE-588)4052023-7 gnd Gebäude (DE-588)4156127-2 gnd |
| subject_GND | (DE-588)4052023-7 (DE-588)4156127-2 |
| title | Sound insulation in buildings |
| title_auth | Sound insulation in buildings |
| title_exact_search | Sound insulation in buildings |
| title_full | Sound insulation in buildings Jens Holger Rindel |
| title_fullStr | Sound insulation in buildings Jens Holger Rindel |
| title_full_unstemmed | Sound insulation in buildings Jens Holger Rindel |
| title_short | Sound insulation in buildings |
| title_sort | sound insulation in buildings |
| topic | Soundproofing Schalldämmung (DE-588)4052023-7 gnd Gebäude (DE-588)4156127-2 gnd |
| topic_facet | Soundproofing Schalldämmung Gebäude |
| url | https://doi.org/10.1201/9781351228206 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030382268&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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