The Zebrafish: Genetics, Genomics, and Transcriptomics

Professor of Biochemistry and Marine Biology at Northeastern University, promoted 1996. Joined Northeastern faculty in 1987. Previously a faculty member in Dept. of Biochemistry at the University of Mississippi Medical Center, 1983-1987.Principal Investigator in the U.S. Antarctic Program since 1984. Twelve field seasons "on the ice" since 1981. Research conducted at Palmer Station, Antarctica, and McMurdo Station, Antarctica.Research areas: Biochemical, cellular, and physiological adaptation to low and high temperatures. Structure and function of cytoplasmic microtubules and microtubule-dependent motors from cold-adapted Antarctic fishes. Regulation of tubulin and globin gene expression in zebrafish and Antarctic fishes. Role of microtubules in morphogenesis of the zebrafish embryo. Developmental hemapoiesis in zebrafish and Antarctic fishes. UV-induced DNA damage and repair in Antarctic marine organisms. Grousbeck Professor of Pediatrics, Boston Children's Hospital / HHMI, Boston, MA, USA Professor, Department of Biology, Institute of Neuroscience, University of Oregon, Eugene, OR, USA

Part 1. Forward and Reverse Genetics 1. Multiplex Conditional Mutagenesis in Zebra?sh Using the CRISPR/Cas System 2. Tol2-Mediated Transgenesis, Gene Trapping and Enhancer Trapping, and the Gal4-UAS System 3. Genetic Screens for Mutations Affecting Adult Traits and Parental-Effect Genes 4. Targeted Candidate Gene Screens Using CRISPR/Cas9 Technology 5. TALEN and CRISPR Enhanced DNA Homologous Recombination for Gene Editing in Zebrafish 6. Precise Genome Editing by Homologous Recombination 7. The Zebrafish Genome Editing Toolkit 8. Clonal Analysis of Gene Loss-of-function and Tissue-specific Gene Deletion in Zebrafish via CRISPR/Cas9 Technology 9. Tissue-Specific Gene Targeting Using CRISPR/Cas9

Part 2. Transgenesis and Functional Genomics 10. Transcriptional Regulation Using the Q System in Transgenic Zebrafish 11. Contemporary Zebrafish Transgenesis with Tol2 and Application for Cre/lox Recombination Experiments 12. Method  for Somatic Cell Nuclear Transfer in Zebrafish 13. Experimental Approaches to Studying the Nature and Impact of Splicing Variation in Zebrafish 14. PICCORO: A Technique for Manipulating the Activity of Transcription Factors with Blue Light

Part 3. Transcriptomics 15. Tomo-seq: A Method to Obtain Genome-Wide Expression Data with Spatial Resolution 16. Cell-Type Specific Transcriptomic Analysis by Thiouracil Tagging in Zebrafish 17. RT-qPCR Gene Expression Analysis in Zebrafish: Preanalytical Precautions and Use of Expressed Repetitive Elements (ERE) for Normalization

Part 4. Epigenetics 18. Genome-Wide DNA Methylation Profiling in Zebrafish 19. Histone Modifications in Zebrafish Development 20. Chromatin Immunoprecipitation and an Open Chromatin Assay in Zebrafish Erythrocytes 21. Assay for Transposase-Accessible Chromatin and Circularized Chromosome Conformation Capture, Two Methods to Explore the Regulatory Landscapes of Genes in Zebrafish 22. Epigenetic Regulation of Hematopoietic Stem Cell Development

Part 5. Zebrafish Infrastructure 23. A Scientist’s Guide for Submitting Data to ZFIN 24. New Frontiers for Zebrafish Management 25. Aquaculture, Husbandry, and Shipping at the Zebrafish International Resource Center 26. Health Monitoring and Disease Prevention at the Zebrafish International Resource Center