The Zebrafish Genetics Genomics and Transcriptomics 4th Edition by H William Detrich, Monte Westerfield, Leonard I Zon ISBN 0128034742 9780128034743

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ISBN 10: 0128034742 
ISBN 13: 9780128034743
Author: H William Detrich, Monte Westerfield, Leonard I Zon

The Zebrafish Genetics Genomics and Transcriptomics 4th Table of contents:

Part 1: Forward and Reverse Genetics
Chapter 1. Multiplex conditional mutagenesis in zebrafish using the CRISPR/Cas system
Introduction
1. Methods
2. Discussion
Summary
Chapter 2. Tol2-mediated transgenesis, gene trapping, enhancer trapping, and Gal4-UAS system
Introduction
1. Transgenesis by Using the Tol2 Transposable Element
2. Gene Trap, Enhancer Trap Methods for the Gal4FF-UAS Methods
3. Targeted Gene Expression With the Gal4-UAS System
Chapter 3. Genetic screens for mutations affecting adult traits and parental-effect genes
Introduction
1. Strategies for Adult Trait and Parental-Effect Screens
2. Selection of Lines for Genetic Screens
3. Recovery and Maintenance of Adult and Parental-Effect Mutations
4. Mapping Adult and Parental-Effect Mutations, and Cloning the Mutant Gene
5. Solutions, Materials, and Protocols
Conclusions
Chapter 4. Targeted candidate gene screens using CRISPR/Cas9 technology
Introduction
1. General Considerations Before Starting a CRISPR Screen
2. Considerations for the Cas9 Enzyme
3. Cas9 Synthesis Protocol
4. Considerations for Choosing sgRNA Target Sites
5. Designing an sgRNA
6. sgRNA Design and Synthesis
7. sgRNA Synthesis Protocol
8. Identifying Injection Conditions to Use for the Screen
9. Assaying the Rate of Mutagenesis in F0-Injected Embryos
10. Confirmation of Phenotypes
11. Summary
Chapter 5. TALEN- and CRISPR-enhanced DNA homologous recombination for gene editing in zebrafish
Introduction
1. Materials
2. Methods
Summary
Chapter 6. Precise genome editing by homologous recombination
Introduction
1. Overview of Contemporary Approaches to Genome Editing
2. Summary of Workflow
3. Factors to Consider for Genome Editing Via Homologous Recombination
4. Method of Approach
Conclusions
Chapter 7. The zebrafish genome editing toolkit
Introduction
1. Reagents
2. DNA Repair Mechanisms—the Rise of Mutations
3. Microinjection
4. Screening for F0 Mutants
5. Selecting for Desirable F1 Mutants
Conclusion
Chapter 8. Clonal analysis of gene loss of function and tissue-specific gene deletion in zebrafish via CRISPR/Cas9 technology
Introduction
1. Methods for Tissue-Specific Gene Inactivation and Clonal Analysis of Mutant Cells
2. Discussion
Chapter 9. Tissue-specific gene targeting using CRISPR/Cas9
Introduction
1. Rationale
2. Methods
3. Discussion
Part 2: Transgenesis and Functional Genomics
Chapter 10. Transcriptional regulation using the Q system in transgenic zebrafish
1. Background
2. Components of the Q Transcriptional Regulatory System
3. Gene/Enhancer Trapping Using the Q System
4. Future Prospects
Chapter 11. Contemporary zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments
1. Introduction
2. Transgene Design, Cloning, and Transgenesis
3. Tol2 Transgene Genetics
4. CreERT2-Controlled lox Recombination Using 4-OHT
5. Beyond Traditional Cre/lox Lineage Tracing
6. Discussion
Chapter 12. Method for somatic cell nuclear transfer in zebrafish
Introduction
1. Materials
2. Method
Chapter 13. Experimental approaches to studying the nature and impact of splicing variation in zebrafish
1. Overview of RNA Splicing
2. Employing Zebrafish Models for Studying Splicing Variation
3. Tools for Global Spliceome Analysis in Zebrafish
4. Biochemical Analysis of Spliceosome Component Assembly
5. Assessing the Biological Impact of Splicing Variation or Dysfunction in Zebrafish
6. Summary
Chapter 14. PICCORO: A technique for manipulating the activity of transcription factors with blue light
Introduction
1. Mechanism of PICCORO
2. Method for Constructing a PICCORO Plasmid
Conclusion
Part 3: Transcriptomics
Chapter 15. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution
Introduction
1. Tissue Extraction and Embedding
2. Cryosectioning and Trizol Extraction
3. cDNA Synthesis
4. In Vitro Transcription
5. Library Preparation
6. Data Analysis
Summary and Conclusions
Chapter 16. Cell type-specific transcriptomic analysis by thiouracil tagging in zebrafish
Introduction
1. Part 1. Establishing and Characterizing a Cell Type-Restricted UPRT Transgenic Line of Fish
2. Part 2. Experimental Design and 4TU Treatments
3. Part 3. RNA Manipulations, Biotinylation, and Purification
4. Part 4: RNA Sequencing, Data Analysis, and Validation
Conclusions
Chapter 17. RT-qPCR gene expression analysis in zebrafish: Preanalytical precautions and use of expressed repetitive elements for normalization
Introduction
1. Sample Collection, RNA Extraction and Quality Control, and Reverse Transcription
2. Assay Design and Quality Control
3. Reference Target Validation
4. Expressed Repeat RT-qPCR Normalization in Zebrafish
Part 4: Epigenetics
Chapter 18. Genome-wide DNA methylation profiling in zebrafish
Introduction
1. Rationale
2. Methods
Discussion and Conclusions
Chapter 19. Histone modifications in zebrafish development
Introduction
1. Recent Progress in Understanding the Roles of Histone Modifications in Zebrafish Development
2. Chromatin Immunoprecipitation From Zebrafish Embryos
3. High-Throughput Whole-Genome DNA Sequencing and Integrative Analysis of Epigenomic Data
Conclusions and Prospects
Chapter 20. Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes
Introduction
1. Rationale
2. Adult Zebrafish Exsanguination
3. Chromatin Immunoprecipitation and ChIP-seq Library Construction
4. ATAC-seq Analysis of Open Chromatin Regions
5. ChIP-seq and ATAC-seq Data Analysis
6. Results
Summary and Conclusion
Chapter 21. Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish
Introduction
1. 4C-seq Protocol
2. ATAC-seq Protocol
Chapter 22. Epigenetic regulation of hematopoietic stem cell development
Introduction
1. Mechanisms of Epigenetic Regulation
2. Hematopoietic Stem Cell Development
3. Approaches
4. Disease Models
5. Current Challenges and Future Directions
Conclusions
Part 5: Zebrafish Infrastructure
Chapter 23. A scientist’s guide for submitting data to ZFIN
Introduction
1. Why Load Data Into ZFIN?
2. The Structure of the ZFIN Database
3. The Data Submission Process
4. Data Submissions
5. What Happens to Your Data After Submission to ZFIN?
6. Data Submission Templates
Funding Information
Chapter 24. New frontiers for zebrafish management
Introduction
1. Physicochemical Environment
2. Nutrition and Feeding
3. Breeding
4. Genetic Management
5. Larviculture
6. Health Management
7. Housing/Aquaculture
8. Welfare
9. Education and Training
10. Commercial Provision of Model Infrastructural Services
Summary
Chapter 25. Aquaculture, husbandry, and shipping at the Zebrafish International Resource Center
Introduction
1. Methods
2. Materials
Chapter 26. Health monitoring and disease prevention at the Zebrafish International Resource Center
Introduction
1. Methods
2. Materials

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Tags: H William Detrich, Monte Westerfield, Leonard I Zon, Zebrafish Genetics