Human pluripotent stem cell derived organoid models / edited by Jason R. Spence. -- Cambridge, MA : Academic Press, 2020. – (58.1574/M592/v.159)

Contents

Contributors
CHAPTER 1  Generation of esophageal organoids and organotypic raft cultures from human pluripotent stem cells
              1. Introduction
              2. Significance and applications
              3. Morphological and transcriptional analysis of developing esophageal cultures
              4. Overview of differentiation protocol
              5. Step-by-step protocol
              6. Future directions
              7. Summary
              Acknowledgments
              References
CHAPTER 2 Generation and use of gastric organoids for the study of Helicobacter pylori pathogenesis
              1. Introduction
              2. Significance and applications of gastric organoids
              3. Overview of the protocol
              4. Step-by-step protocol
              5. Precursor techniques
              6. Safety considerations and standards
              7. Analysis of cultures
              8. Alternative methods/procedures
              9. Summary
              Acknowledgments
              References
CHAPTER 3 Generation of multi-cellular human liver organoids from pluripotent stem cells
              1. Introduction
              2. Applications of liver organoids
              3. Overview of differentiation protocol
              4. Step-by-step methods
              5. Technical and design considerations
              6. Conclusions
              Acknowledgments
              References
CHAPTER 4 Pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids
              1. Introduction
              2. Physiology of cholangiocytes
              3. Biliary differentiation during development
              4. Human cholangiocyte sources for organoids
              5. Applications of pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids
              6. Overview of the protocol
              7. Step-by-step methods
              8. Conclusion
              Acknowledgments
              References
CHAPTER 5 Differentiation of human airway-organoids from induced pluripotent stem cells (iPSCs)
              1. Introduction
              2. iPSC-derived airway organoid cell types
              3. Applications of airway organoids
              4. Overview of differentiation protocol
              5. Step-by-step methods
              6. Conclusion
              References
CHAPTER 6 A method of generating alveolar organoids using human pluripotent stem cells
              1. Introduction
              2. Discovery of alveolar organoids
              3. Need of AOs using human ESCs and iPSCs
              4. Overview of lung cell differentiation from hPSCs
              5. Alveolar organoid cell types
              6. Overview of the differentiation protocol
              7. Step-by-step methods
              8. Passage of AOs for long-term culture (fibroblast-dependent).
              9. Differentiation of lung progenitor cells into fibroblast-free (FF) AOs
             10. Immunofluorescent analysis of organoids
             11. The transmission electron microscopic analysis of AT2 cells.
             12. Technical and design considerations
             13. Conclusion
             Acknowledgments
             References
CHAPTER 7 Generation of small intestinal organoids for experimental intestinal physiology
              1. Introduction
              2. Applications of intestinal organoids
              3. Overview of differentiation protocol
              4. Materials, equipment and reagents
              5. Organoid differentiation protocol
              6. Application of HIOs, and variations on HIO culture
              7. Pros and cons of pluripotent stem cell derived intestinal organoids
              8. Troubleshooting and optimization
              9. Related techniques
             10. Ethical considerations and standards
             11. Conclusions
             References
CHAPTER 8 Pluripotent stem cell derived intestinal organoids with an enteric nervous system
              1. Introduction
              2. Applications of intestinal organoids with an enteric nervous system
              3. Protocol overview
              4. Step by step methods
              5. Troubleshooting and optimization
              6. Precursor and alternative techniques
              7. Summary
              Acknowledgments
              References
CHAPTER 9 Generation of human colonic organoids from human pluripotent stem cells
              1. Introduction
              2. Applications of human colonic organoids
              3. Overview of HCO differentiation protocol
             4. Step-by-step protocol
              5. Statistical analysis
              6. Pros and cons
              7. Troubleshooting and optimization
              8. Conclusion
              References
CHAPTER 10 Single-cell genomic analysis of human cerebral organoids
              1. Introduction
             2. Overview of the protocol
              3. Generating single-cell sequencing data from cerebral organoids
             4. Basic analysis of organoid scRNA-seq data
              5. Conclusions and outlook
              Acknowledgments
              References
              Further reading
              Overview of computational tools for single-cell analysis
              Best practices in single-cell RNA-seq analysis
              Benchmark batch correction methods
              Experimental design to reduce batch effects in single-cell  RNA-seq experiments
              Trajectory inference benchmark study
CHAPTER 11 Generating ventral spinal organoids from human induced pluripotent stem cells
              1. Introduction
              2. Spinal cord development
              3. Applications of spinal cord organoids
              4. Overview of the differentiation protocol
              5. Step-by-step methods
              6. Technical and design considerations
              7. Conclusion
              Acknowledgments
              References
CHAPTER 12 Differentiation of retinal organoids from human pluripotent stem cells
              1. Introduction
              2. Application of retinal organoids
              3. Cell types found within retinal organoids
              4. Overview of differentiation protocol
              5. Step-by-step methods
              6. Technical and design considerations
              7. Conclusions
              Acknowledgments
              References
CHAPTER 13 Generation of inner ear organoids from human pluripotent stem cells
              1. Introduction
              2. Overview of the differentiation protocol
              3. Applications of inner ear organoids
              4. Materials
              5. Protocol
              6. Characterization of inner ear organoids
              7. Notes
              8. Safety considerations
              Acknowledgments
              References