Guide to Techniques in Mouse Development, Part B

ContributorsPrefaceVolumes in SeriesSection I. Transgenesis 1. Lentivirus Transgenesis 1. Introduction 2. Generation of Lentiviral Vectors 3. Generation of Transgenic Animals with Lentiviral Vectors 4. Characterization of Transgenic Animals 5. Summary Acknowledgments References 2. Germline Modification Using Mouse Spermatogonial Stem Cells 1. Introduction 2. Establishing and Maintaining a GS Cell Culture 3. Gene Transduction and Genetic Selection of GS Cells 4. Spermatogonial Transplantation and Offspring Production References 3. Embryonic In Vivo Electroporation in the Mouse 1. Introduction 2. Materials 3. In Utero Electroporation 4. Exo Utero Electroporation 5. Analysis of Electroporated Mice Acknowledgments ReferencesSection II. Transposons 4. Current Applications of Transposons in Mouse Genetics 1. Introduction 2. Molecular Characteristics of TEs with Activity in Mice 3. Applications of TEs in Mouse Genetics 4. The Future of TEs in Mouse Genetics References 5. Functional Genomics in the Mouse using the Sleeping Beauty Transposon System 1. Introduction 2. Genome-Wide Germline Mutagenesis with the SB Transgenic Approach 3. Region-Specific Chromosome Engineering with the SB Knock-in Approach 4. Concluding Remarks Acknowledgments References 6. The Use of DNA Transposons for Cancer Gene Discovery in Mice 1. Introduction 2. Choice of Transposon 3. Transposon Design for Cancer Screens 4. Whole-Body (Constitutive) Screens 5. Tissue-Specific Mutagenesis 6. Inducible Transposase Expression 7. Mapping of Transposon Integration Sites 8. Statistical Mining of Recurrent Integration Sites 9. Validation of Putative Cancer Genes 10. Idiosyncrasies of Transposons as Cancer Gene Discovery Tools 11. Concluding Remarks ReferencesSection III. Recombinases 7. A Practical Summary of Site-Specific Recombination, Conditional Mutagenesis, and Tamoxifen Induction of CreERT2 1. Introduction 2. Recombinase Target Sites 3. Applications 4. Allele Design 5. Recombinase Properties 6. Tamoxifen Administration in Mice and Cultured Cells 7. Problems 8. Concluding Remarks Acknowledgments References 8. A Recombineering Pipeline to Make Conditional Targeting Constructs 1. Introduction 2. Recombineering 3. Methods 4. Standard Recombineering Electroporation Protocol 5. Concluding Remarks Acknowledgments References 9. Confirmation of Recombination Site Functionality in Gene Targeting Vectors using Recombinase-Expressing Bacteria 1. Introduction 2. Materials 3. Method 4. Example of Results 5. Summary Acknowledgments References 10. Genetic Fate Mapping Using Site-Specific Recombinases 1. Principles Behind Genetic Fate Mapping 2. Genetic Fate Mapping Technique 3. Future Applications: Combining Genetic Fate Mapping with Mutant Analysis References 11. Mapping Cell Fate and Function Using Recombinase-Based Intersectional Strategies 1. Introduction 2. Accessing Mouse Embryonic Cells In Utero for Tracer Molecule ‘‘Delivery’’ Using Transgenesis and Site-Specific DNA Recombination 3. Improving Cell-Subtype Selectivity in Genetic Fate Maps Using a Dual-Recombinase Intersectional Method 4. Transgenes Enabling Subtractive as well as Intersectional Genetic Fate Mapping 5. Exploiting Different Reporter Molecules to Reveal Different Features of Mapped Cell Populations 6. 3 for 1 7. Intersectional Transgene Activation Reaches from Mapping Cell Fate to Mapping Cell Function 8. Methods and Materials 9. Concluding Remarks Acknowledgments ReferencesSection IV. Mutagenesis 12. Genome-Wide Forward Genetic Screens in Mouse ES Cells 1. Introduction 2. Strategies for Genome-Wide Mutagenesis 3. Using Blm-Deficient ES Cells to Conduct Recessive Genetic Screens 4. Mutant Validation 5. Concluding Remarks Acknowledgments References 13. Gene Trap Mutagenesis in the Mouse 1. Introduction 2. Gene Trapping Strategies 3. Design of the Gene Trap Vector 4. Gene Trapping Protocol for Retroviral Vectors 5. Gene Trapping Protocol for Transposon Vectors 6. Identification of Trap Insertion Sites by Splinkerette PCR 7. Ordering and Handling of Gene Trap Clones from Consortia 8. Outlook Acknowledgments References 14. A Wider Context for Gene Trap Mutagenesis 1. Introduction 2. Gene Trap Vectors 3. Random Integration as a Means to Generate New Mutations 4. Targeted Trapping 5. Public Resources of Mutagenized ES Cell Clones 6. Gene Discovery and Annotation 7. Hypothesis-Driven Screens 8. Protocols Acknowledgments References 15. Mouse Mutagenesis with the Chemical Supermutagen ENU 1. Introduction 2. Materials and Methods 3. Conclusion Acknowledgments References 16. Phenotype-Driven Mouse ENU Mutagenesis Screens 1. Introduction 2. Screen Design 3. Screen Execution 4. Gene Identification 5. The Future for Mouse Forward Genetics References 17. Using ENU Mutagenesis for Phenotype-Driven Analysis of the Mouse 1. Introduction 2. ENU Screen Design 3. ENU Treatment 4. Mutant Ascertainment 5. Mutation Identification 6. Mutation Validation 7. Summary ReferencesSection V. Gene Knockdowns 18. Exploration of Self-Renewal and Pluripotency in ES Cells Using RNAi 1. Introduction 2. Maintenance of Mouse Embryonic Stem Cells 3. siRNA-Mediated Gene Knockdown 4. Lentivirus-Based shRNA Knockdown System 5. Concluding Remarks References 19. Transgenic RNAi Applications in the Mouse 1. Introduction 2. Short Interfering RNAs 3. Short Hairpin RNA Expression Vectors 4. Transgenic shRNA Expression In Vivo 5. Conditional RNAi 6. Experimental Protocols References 20. Gene Knockdown in the Mouse Through RNAi 1. Introduction 2. Principle of the Approach 3. Materials 4. Methods 5. Concluding Remarks Acknowledgments References 21. In Vivo Analysis of Gene Knockdown in Tetracycline-Inducible shRNA Mice 1. Introduction 2. Methods 3. Notes References 22. The Power of Reversibility: Regulating Gene Activities via Tetracycline-Controlled Transcription 1. Introduction 2. The Tet Regulatory Systems 3. Tet-Transgenic Mice Available from Repositories 4. Tet-Controlled Transgenes to Study Learning and Memory 5. Tet-Transgenic Animals in Cancer Research 6. Secondary iPSC Technology 7. Transgenic Rats 8. Future Perspectives ReferencesSection VI. Gene Expression Profiling 23. Gene Expression Profiling of Mouse Oocytes and Preimplantation Embryos 1. Introduction 2. Experimental Design Considerations 3. RNA Isolation and cRNA Target Preparation Protocol (Based on the Affymetrix Protocol for Eukaryotic Small Sample Target Labeling Assay Version II) 4. Quality Control Assessment of cRNA 5. Methods for Microarray Data Analysis 6. Validation Methods 7. Archiving Results 8. Future Directions Acknowledgments References 24. Interrogating the Transcriptome of Oocytes and Preimplantation Embryos 1. Introduction 2. RNA Relative Quantification in Oocytes and Preimplantation Embryos 3. Comparative Analysis of Large-Scale Expression Analyses 4. Taking Isoform-Specific Changes into Account 5. Concluding Remarks Acknowledgments References 25. Gene Expression Profiling of Mouse Embryos with Microarrays 1. Introduction 2. Considerations for Methods of Gene Expression Profiling 3. Experimental Strategies 4. Expression Profiling of Small Amounts of RNAs 5. QC of Microarray Results 6. Analysis and Interpretation of Microarray Data 7. Submitting the Data to the Public Database Acknowledgments ReferencesAuthor IndexSubject Index