The zebrafish: genetics, genomics, and transcriptomics:
Saved in:
| Other Authors: | , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam
Elsevier, Academic Press
2016
|
| Series: | Methods in cell biology
Volume 135 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Bis zur 3. Auflage andere Bandeinteilung |
| Physical Description: | xxxvi, 577 Seiten, 13 ungezählte Seiten Illustrationen |
| ISBN: | 9780128034743 |
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Record in the Search Index
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| adam_text | Contents
Contributors...................................................xvii
Preface........................................................xxv
PART I FORWARD AND REVERSE GENETICS
CHAPTER 1 Multiplex conditional mutagenesis in zebrafish
using the CRISPR/Cas system...............................3
L. Yin, L.A. Maddison, W. Chen
Introduction..............................................4
1. Methods...................................................5
2. Discussion..............................................14
Summary..................................................14
Acknowledgments..........................................15
References............................................. 15
CHAPTER 2 70/2-mediated transgenesis, gene trapping,
enhancer trapping, and Gal4-UAS system...................19
K. Kawakami, K. Asakawa, A. Muto, H. Wada
Introduction.............................................20
1. Transgenesis by Using the Toll Transposable Element...21
2- Gene Trap, Enhancer Trap Methods for the Gal4FF-UAS
Methods..................................................27
3. Targeted Gene Expression With the Gal4-UAS System......32
Acknowledgments..........................................36
References...............................................36
CHAPTER 3 Genetic screens for mutations affecting adult
traits and parental-effect genes.........................39
F. Pelegri, M.C. Mullins
Introduction............................................ 41
1. Strategies for Adult Trait and Parental-Effect Screens...48
2. Selection of Lines for Genetic Screens................. 62
3. Recovery and Maintenance of Adult and Parental-Effect
Mutations................................................65
4. Mapping Adult and Parental-Effect Mutations, and Cloning
the Mutant Gene..........................................70
viii Contents
5. Solutions, Materials, and Protocols...................75
Conclusions.............................................80
Acknowledgments.........................................80
References..............................................81
CHAPTER 4 Targeted candidate gene screens using
CRISPR/Cas9 technology............................... 89
A.N. Shah, C.B. Moens, A.C. Miller
Introduction............................................90
1. General Considerations Before Starting a CRISPR Screen.92
2. Considerations for the Cas9 Enzyme....................92
3. Cas9 Synthesis Protocol...............................94
4. Considerations for Choosing sgRNA Target Sites........95
5. Designing an sgRNA....................................96
6. sgRNA Design and Synthesis............................97
7. sgRNA Synthesis Protocol..............................98
8. Identifying Injection Conditions to Use for the Screen.100
9. Assaying the Rate of Mutagenesis in Fo-Injected Embryos.. 101
10. Confirmation of Phenotypes...........................102
11, Summary..............................................104
References.............................................104
CHAPTER 5 TALEN- and CRISPR-enhanced DNA homologous
recombination for gene editing in zebrafish............107
Y. Zhang, H. Huang, B. Zhang, S. Lin
Introduction...........................................108
1. Materials............................................112
2. Methods..............................................113
Summary................................................117
Acknowledgments........................................118
References.............................................118
CHAPTER 6 Precise genome editing by homologous
recombination..........................................121
K. Hoshijima, M.J. Jurynec, D.J. Grunwald
Introduction...........................................122
1. Overview of Contemporary Approaches to Genome Editing.. 123
2. Summary of Workflow..................................128
Contents ix
3. Factors to Consider for Genome Editing Via Homologous
Recombination..........................................129
4. Method of Approach.....................................133
Conclusions............................................144
Acknowledgments........................................145
References.............................................145
CHAPTER 7 The zebrafish genome editing toolkit........................149
H. Ata, K.J. Clark, S.C. Ekker
Introduction...........................................150
1. Reagents...............................................152
2. DNA Repair Mechanisms—the Rise of Mutations............156
3. Microinjection.........................................158
4. Screening for F0 Mutants...............................159
5. Selecting for Desirable FI Mutants.....................161
Conclusion.............................................165
References.............................................166
CHAPTER 8 Clonal analysis of gene loss of function and
tissue-specific gene deletion in zebrafish via
CRISPR/Cas9 technology.................................171
F. De Santis, V. Di Donato, F. Del Bene
Introduction...........................................172
1. Methods for Tissue-Specific Gene Inactivation and Clonal
Analysis of Mutant Cells...............................175
2. Discussion.............................................185
References.............................................186
CHAPTER 9 Tissue-specific gene targeting using
CR!SPR/Cas9.......................................... 189
J. Ablain, L.l. Zon
Introduction...........................................190
1. Rationale............................................ 191
2. Methods................................................193
3. Discussion.............................................197
Acknowledgments........................................199
References.............................................199
X
Contents
PART II TRANSGENESIS AND FUNCTIONAL GENOMICS
CHAPTER 10 Transcriptional regulation using the Q system in
transgenic zebrafish..................................205
A. Ghosh, M.E. Halpern
1. Background...........................................206
2. Components of the Q Transcriptional Regulatory System.208
3. Gene/Enhancer Trapping Using the Q System............213
4. Future Prospects.....................................214
Acknowledgments.......................................215
References............................................215
CHAPTER 11 Contemporary zebrafish transgenesis with Tol2
and application for Cr recombination
experiments...........................................219
A. Felker, C. Mosimann
1. Introduction.........................................220
2. Transgene Design, Cloning, and Transgenesis..........224
3. Tol2 Transgene Genetics..............................229
4. CreERT2-Controlled lox Recombination Using 4-OHT......234
5. Beyond Traditional Cr e/lox Lineage Tracing..........236
6. Discussion...........................................239
Acknowledgments.......................................239
References............................................239
CHAPTER 12 Method for somatic cell nuclear transfer in
zebrafish.............................................245
K. Siripattarapravat, S. Prukudom, J. Cibelli
Introduction..........................................246
1. Materials............................................246
2. Method...............................................251
Acknowledgments.......................................256
References............................................257
CHAPTER 13 Experimental approaches to studying the nature
and impact of splicing variation in zebrafish.........259
M.C. Keightley, S. Markmiller, C.G. Love, J.E.J. Rasko,
G.J. Lieschke, J.K. Heath
1. Overview of RNA Splicing..............................260
Contents xi
2. Employing Zebrafish Models for Studying Splicing
Variation...........................................266
3. Tools for Global Spliceome Analysis in Zebrafish...269
4. Biochemical Analysis of Spliceosome Component
Assembly............................................274
5. Assessing the Biological Impact of Splicing Variation or
Dysfunction in Zebrafish............................276
6. Summary............................................278
Acknowledgments.....................................279
References..........................................279
CHAPTER 14 PICCORO: A technique for manipulating the
activity of transcription factors with blue light..289
S. Masuda, M. Tanaka
Introduction........................................290
1. Mechanism of PICCORO...............................290
2. Method for Constructing a PICCORO Plasmid..........292
Conclusion..........................................294
References..........................................294
PART III TRANSCRIPTOMICS
CHAPTER 15 Tomchseq: a method to obtain genome-wide
expression data with spatial resolution..................299
F. Kruse, i.P. Junker, A. van Oudenaarden, J. Bakkers
Introduction.............................................300
1. Tissue Extraction and Embedding.........................300
2. Cryosectioning and Trizol Extraction....................301
3. cDNA Synthesis..........................................302
4. In Vitro Transcription..................................302
5. Library Preparation.......*............................303
6. Data Analysis...........................................304
Summary and Conclusions..................................305
References...............................................306
CHAPTER 16 Cell type-specific transcriptomic analysis
by thiouracil tagging in zebrafish.......................309
T. Erickson, T. Nicolson
Introduction.............................................310
1. Part 1. Establishing and Characterizing a Cell
Type-Restricted UPRT Transgenic Line of Fish.............312
Contents
2. Part 2. Experimental Design and 4TU Treatments..........319
3. Part 3. RNA Manipulations, Biotinylation, and Purification... 321
4. Part 4: RNA Sequencing, Data Analysis, and Validation...323
Conclusions..............................................324
References...............................................325
CHAPTER 17 RT-qPCR gene expression analysis in zebrafish:
preanalytical precautions and use of expressed
repetitive elements for normalization....................329
S. Vanhauwaert, S. Lefever, P. Coucke, F. Speleman,
A. De Paepe, i. Vandesompele, A. Willaert
Introduction.............................................330
1. Sample Collection, RNA Extraction and Quality Control,
and Reverse Transcription................................331
2. Assay Design and Quality Control........................334
3. Reference Target Validation.............................337
4. Expressed Repeat RT-qPCR Normalization in Zebrafish.....338
References...............................................341
PART IV EPIGENETICS
CHAPTER 18 Genome-wide DNA méthylation profiling in
zebrafish...............................................345
P.l. Murphy, B.R. Cairns
Introduction............................................346
1. Rationale..............................................353
2. Methods................................................353
Discussion and Conclusions..............................357
References..............................................357
CHAPTER 19 Histone modifications in zebrafish development..,.361
V.T. Cunliffe
Introduction............................................363
1. Recent Progress in Understanding the Roles of Histone
Modifications in Zebrafish Development..................368
2. Chromatin Immunoprécipitation From Zebrafish Embryos..372
3. High-Throughput Whole-Genome DNA Sequencing and
Integrative Analysis of Epigenomic Data.................379
Contents xiii
Conclusions and Prospects.............................382
Acknowledgments.......................................382
References............................................382
CHAPTER 20 Chromatin immunoprécipitation and an open
chromatin assay in zebrafish erythrocytes.............387
S. Yang, C.i. Ott, M.P. Rossmann, M. Superdock,
L.l. Zon, Y. Zhou
introduction..........................................388
1. Rationale............................................389
2. Adult Zebrafish Exsanguination.......................390
3. Chromatin Immunoprécipitation and ChIP-seq Library
Construction..........................................391
4. ATAC-seq Analysis of Open Chromatin Regions..........396
5. ChIP-seq and ATAC-seq Data Analysis..................401
6. Results..............................................406
Summary and Conclusion................................406
Acknowledgments.......................................407
References............................................407
CHAPTER 21 Assay for transposase-accessible chromatin
and circularized chromosome conformation
capture, two methods to explore the regulatory
landscapes of genes in zebrafish......................413
A. Fernandez-Minân, J. Bessa, J.J. Tena,
J.L. Gomez-Skarmeta
Introduction..........................................414
1. 4C-seq Protocol......................................418
2. ATAC-seq Protocol....................................425
Acknowledgments.......................................428
References............................................429
CHAPTER 22 Epigenetic regulation of hematopoietic stem
cell development......................................431
C. Li, T. Evans, M.G. Goll
Introduction..........................................432
1. Mechanisms of Epigenetic Regulation..................432
2. Hematopoietic Stem Cell Development..................434
3. Approaches...........................................435
4. Disease Models.......................................441
xiv Contents
5. Current Challenges and Future Directions.......442
Conclusions.....................................443
References......................................444
PART V ZEBRAFISH INFRASTRUCTURE
CHAPTER 23 A scientist’s guide for submitting data to ZFIN.............451
D.G. Howe, Y.M. Bradford, A. Eagle, D. Fashena, K. Frazer,
P. Kalita, P. Mani, R. Martin, S.T. Moxon, H. Paddock,
C. Pich, S. Ramachandran, L. Ruzicka, K. Schaper,
X. Shao, A. Singer, S. Toro, C. Van Slyke, M. Westerfield
Introduction...........................................453
1. Why Load Data Into ZFIN?...............................454
2. The Structure of the ZFIN Database.....................454
3. The Data Submission Process............................455
4. Data Submissions.......................................455
5. What Happens to Your Data After Submission to ZFIN?.....477
6. Data Submission Templates..............................478
Funding Information....................................480
References........................*.....................480
CHAPTER 24 New frontiers for zebrafish management......................483
C. Lawrence
Introduction...........................................484
1. Physicochemical Environment...........................485
2. Nutrition and Feeding.................................486
3. Breeding..............................................488
4. Genetic Management....................................489
5. Larviculture..........................................490
6. Health Management.....................................492
7. Housing/Aquaculture...................................494
8. Welfare...............................................495
9. Education and Training................................497
10. Commercial Provision of Model Infrastructural Services.497
Summary.............................................. 498
References........................................... 498
Contents xv
CHAPTER 25 Aquaculture, husbandry, and shipping at
the Zebrafish international Resource Center...........509
Z.M. Varga
Introduction...........................................510
1. Methods................................................512
2. Materials.............................................530
Acknowledgments........................................532
References.............................................532
CHAPTER 26 Health monitoring and disease prevention at the
Zebrafish International Resource Center...............535
Z.M. Varga, K.N. Murray
Introduction...........................................536
1. Methods................................................537
2. Materials.............................................549
References.............................................550
Volumes in Series.....................................................553
Index.................................................................567
|
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| series | Methods in cell biology |
| series2 | Methods in cell biology |
| spelling | The zebrafish: genetics, genomics, and transcriptomics edited by H. William Detrich, III, Monte Westerfield, Leonard I. ZonFourth edition Amsterdam Elsevier, Academic Press 2016 xxxvi, 577 Seiten, 13 ungezählte Seiten Illustrationen txt rdacontent n rdamedia nc rdacarrier Methods in cell biology Volume 135 Bis zur 3. Auflage andere Bandeinteilung Methode (DE-588)4038971-6 gnd rswk-swf Genomik (DE-588)4776397-8 gnd rswk-swf Transkriptomanalyse (DE-588)4775956-2 gnd rswk-swf Zebrabärbling (DE-588)4079468-4 gnd rswk-swf Tiermodell (DE-588)4140660-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Zebrabärbling (DE-588)4079468-4 s Genomik (DE-588)4776397-8 s Transkriptomanalyse (DE-588)4775956-2 s Methode (DE-588)4038971-6 s DE-604 Tiermodell (DE-588)4140660-6 s 1\p DE-604 Detrich, H. William (DE-588)1013514475 edt Westerfield, Monte edt Zon, Leonard I. edt Methods in cell biology Volume 135 (DE-604)BV002534878 135 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029168538&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | The zebrafish: genetics, genomics, and transcriptomics Methods in cell biology Methode (DE-588)4038971-6 gnd Genomik (DE-588)4776397-8 gnd Transkriptomanalyse (DE-588)4775956-2 gnd Zebrabärbling (DE-588)4079468-4 gnd Tiermodell (DE-588)4140660-6 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4776397-8 (DE-588)4775956-2 (DE-588)4079468-4 (DE-588)4140660-6 (DE-588)4143413-4 |
| title | The zebrafish: genetics, genomics, and transcriptomics |
| title_auth | The zebrafish: genetics, genomics, and transcriptomics |
| title_exact_search | The zebrafish: genetics, genomics, and transcriptomics |
| title_full | The zebrafish: genetics, genomics, and transcriptomics edited by H. William Detrich, III, Monte Westerfield, Leonard I. ZonFourth edition |
| title_fullStr | The zebrafish: genetics, genomics, and transcriptomics edited by H. William Detrich, III, Monte Westerfield, Leonard I. ZonFourth edition |
| title_full_unstemmed | The zebrafish: genetics, genomics, and transcriptomics edited by H. William Detrich, III, Monte Westerfield, Leonard I. ZonFourth edition |
| title_short | The zebrafish: genetics, genomics, and transcriptomics |
| title_sort | the zebrafish genetics genomics and transcriptomics |
| topic | Methode (DE-588)4038971-6 gnd Genomik (DE-588)4776397-8 gnd Transkriptomanalyse (DE-588)4775956-2 gnd Zebrabärbling (DE-588)4079468-4 gnd Tiermodell (DE-588)4140660-6 gnd |
| topic_facet | Methode Genomik Transkriptomanalyse Zebrabärbling Tiermodell Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029168538&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV002534878 |
| work_keys_str_mv | AT detrichhwilliam thezebrafishgeneticsgenomicsandtranscriptomics AT westerfieldmonte thezebrafishgeneticsgenomicsandtranscriptomics AT zonleonardi thezebrafishgeneticsgenomicsandtranscriptomics |