Human pluripotent stem cell derived organoid models:
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| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge, MA ; San Diego, CA
Academic Press, an imprint of Elsevier
2020
|
| Edition: | First edition |
| Series: | Methods in cell biology
Volume 159 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xiv, 321 Seiten Illustrationen, Diagramme |
| ISBN: | 9780128215319 |
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| adam_text | Contents Contributors............................................................................................................. xi CHAPTER 1 Generation of esophageal organoids and organotypic raft cultures from human pluripotent stem cells........................................................................1 Vered Shacham-Silverberg and James M. Wells 1. Introduction.................................................................................... 2 2. Significance and applications.........................................................3 3. Morphological and transcriptional analysis of developing esophageal cultures........................................................................ 4 4. Overview of differentiation protocol............................................. 5 5. Step-by-step protocol..................................................................... 7 6. Future directions...........................................................................19 7. Summary...................................................................................... 20 Acknowledgments............................................................................. 20 References..........................................................................................20 CHAPTER 2 Generation and use of gastric organoids for the study of Helicobacter pylori pathogenesis..........23 Jayati Chakrabarti and Yana Zavros 1. Introduction.................................................................................. 24 2. Significance and applications of gastric
organoids..................... 26 3. Overview of the protocol............................................................. 27 4. Step-by-step protocol................................................................... 27 5. Precursor techniques.................................................................... 38 6. Safety considerations and standards............................................ 39 7. Analysis of cultures..................................................................... 40 8. Alternative methods/procedures.................................................. 41 9. Summary...................................................................................... 44 Acknowledgments............................................................................. 44 References......................................................................................... 44 CHAPTER 3 Generation of multi-cellular human liver organoids from pluripotent stem cells....................... 47 Wendy L. Thompson and Takanori Takebe 1. Introduction.................................................................................. 48 2. Applications of liver organoids....................................................50
VI Contents 3. Overview of differentiation protocol........................................... 51 4. Step-by-step methods....................................................................52 5. Technical and design considerations............................................65 6. Conclusions...................................................................................66 Acknowledgments..............................................................................66 References.......................................................................................... 66 CHAPTER 4 Pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids........................................ 69 Eleanor Luce and Anne Dubart-Kupperschmitt 1. Introduction.................................................................................. 70 2. Physiology of cholangiocytes...................................................... 71 3. Biliary differentiation during development................................. 74 4. Human cholangiocyte sources for organoids...............................75 5. Applications of pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids.............................. 76 6. Overview of the protocol............................................................. 78 7. Step-by-step methods................................................................... 80 8. Conclusion.................................................................................... 89 Acknowledgments.............................................................................
89 References..........................................................................................90 CHAPTER 5 Differentiation of human airway-organoids from induced pluripotent stem cells (iPSCs)............. 95 Ruobing Wang, Katie B. McCauley, Darrell N. Kotton, and Finn Hawkins 1. Introduction.................................................................................. 96 2. iPSC-derived airway organoid cell types.................................... 98 3. Applications of airway organoids................................................99 4. Overview of differentiation protocol......................................... 102 5. Step-by-step methods................................................................. 102 6. Conclusion.................................................................................. 110 References........................................................................................110 CHAPTER 6 A method of generating alveolar organoids using human pluripotent stem cells...........................115 Yuki Yamamoto, Yohei Korogj, Toyohiro Hirai, and Shimpei Gotoh 1. Introduction................................................................................ 116 2. Discovery of alveolar organoids................................................ 117
Contents 3. Need of AOs using human ESCs and iPSCs............................... 118 4. Overview of lung cell differentiation from hPSCs..................... 118 5. 6. 7. 8. Alveolar organoid cell types..........................................................119 Overview of the differentiation protocol......................................119 Step-by-step methods..................................................................... 120 Passage of AOs for long-term culture (fibroblast-dependent)... 129 9. Differentiation of lung progenitor cells into fibroblast-free (FF) AOs................................................................ 131 10. Immunofluorescent analysis of organoids....................................132 11. The transmission electron microscopic analysis of AT2 cells... 134 12. Technical and design considerations............................................ 136 13. Conclusion....................................................................................... 137 Acknowledgments.................................................................................. 138 References............................................................................................... 138 CHAPTER 7 Generation of small intestinal organoids for experimental intestinal physiology...................... 143 Meghan Capeling, Sha Huang, Adriana Mulero-Russe, Roberto Cieza, Yu-Hwai Tsai, Andres Garcia, and David R. Hill 1. Introduction..................................................................................... 145 2. Applications of intestinal
organoids............................................. 145 3. Overview of differentiation protocol............................................146 4. Materials, equipment and reagents............................................... 147 5. Organoid differentiation protocol................................................. 149 6. Application of HIOs, and variations on HIO culture................. 159 7. Pros and cons of pluripotent stem cell derived intestinal organoids......................................................................................... 169 8. Troubleshooting and optimization................................................ 169 9. Related techniques..........................................................................170 10. Ethical considerations and standards............................................ 170 11. Conclusions..................................................................................... 171 References............................................................................................... 171 CHAPTER 8 Pluripotent stem cell derived intestinal organoids with an enteric nervous system..................................175 Elise Loffet, Lisa Brossard, and Maxime M. Mahe 1. Introduction......................................................................................176 2. Applications of intestinal organoids with an enteric nervous system...............................................................................................178 vii
Contents 3. Protocol overview........................................................................178 4. Step by step methods...................................................................180 5. Troubleshooting and optimization.............................................. 195 6. Precursor and alternative techniques.......................................... 196 7. Summary...................................................................................... 197 Acknowledgments............................................................................197 References........................................................................................197 CHAPTER 9 Generation of human colonic organoids from human pluripotent stem cells............................... 201 Abdelkader Daoud and Jorge 0. Muñera 1. Introduction................................................................................. 202 2. Applications of human colonic organoids................................. 203 3. Overview of HCO differentiation protocol................................205 4. Step-by-step protocol..................................................................209 5. Statistical analysis.......................................................................224 6. Pros and cons.............................................................................. 224 7. Troubleshooting and optimization............................................. 225 8. Conclusion...................................................................................225
References........................................................................................ 226 CHAPTER 10 Single-cell genomic analysis of human cerebral organoids................................................................................229 Sabina Kanton, Barbara Treutlein, and J. Gray Camp 1. Introduction.................................................................................230 2. Overview of the protocol........................................................... 232 3. Generating single-cell sequencing data from cerebral organoids.....................................................................................233 4. Basic analysis of organoidscRNA-seq data............................... 240 5. Conclusions and outlook............................................................ 248 Acknowledgments............................................................................249 References........................................................................................ 249 Further reading.................................................................................256 Overview of computational tools for single-cell analysis.............. 256 Best practices in single-cell RNA-seq analysis.............................. 256 Benchmark batch correction methods............................................. 256 Experimental design to reduce batch effects in single-cell RNA-seq experiments................................................................ 256 Trajectory inference benchmark study............................................256
Contents CHAPTER 11 Generating ventral spinal organoids from human induced pluripotent stem cells.........................................257 Jin-Hui Hor and Shi-Yan Ng 1. Introduction.....................................................................................258 2. Spinal cord development............................................................... 259 3. Applications of spinal cord organoids......................................... 263 4. Overview of the differentiation protocol..................................... 265 5. Step-by-step methods.....................................................................265 6. Technical and design considerations............................................273 7. Conclusion...................................................................................... 274 Acknowledgments................................................................................274 References............................................................................................ 274 CHAPTER 12 Differentiation of retinal organoids from human pluripotent stem cells...........................................................279 Clarisse M. Fligor, Kang-Chieh Huang, Sailee S. Lavekar, Kirstin В. VanderWail, and Jason S. Meyer 1. Introduction.....................................................................................280 2. Application of retinal organoids................................................... 281 3. Cell types found within retinal organoids................................... 284 4. Overview of differentiation
protocol............................................286 5. Step-by-step methods.....................................................................287 6. Technical and design considerations............................................295 7. Conclusions..................................................................................... 298 Acknowledgments................................................................................298 References.............................................................................................298 CHAPTER 13 Generation of inner ear organoids from human pluripotent stem cells...........................................................303 Jing Nie and Eri Hashino 1. Introduction..................................................................................... 304 2. Overview of the differentiation protocol..................................... 306 3. Applications of inner ear organoids............................................. 306 4. Materials..........................................................................................308 5. Protocol........................................................................................... 312 6. Characterization of inner ear organoids.......................................317 7. Notes................................................................................................318 8. Safety considerations..................................................................... 320 Acknowledgments................................................................................ 320
References.............................................................................................320 IX
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| adam_txt |
Contents Contributors. xi CHAPTER 1 Generation of esophageal organoids and organotypic raft cultures from human pluripotent stem cells.1 Vered Shacham-Silverberg and James M. Wells 1. Introduction. 2 2. Significance and applications.3 3. Morphological and transcriptional analysis of developing esophageal cultures. 4 4. Overview of differentiation protocol. 5 5. Step-by-step protocol. 7 6. Future directions.19 7. Summary. 20 Acknowledgments. 20 References.20 CHAPTER 2 Generation and use of gastric organoids for the study of Helicobacter pylori pathogenesis.23 Jayati Chakrabarti and Yana Zavros 1. Introduction. 24 2. Significance and applications of gastric
organoids. 26 3. Overview of the protocol. 27 4. Step-by-step protocol. 27 5. Precursor techniques. 38 6. Safety considerations and standards. 39 7. Analysis of cultures. 40 8. Alternative methods/procedures. 41 9. Summary. 44 Acknowledgments. 44 References. 44 CHAPTER 3 Generation of multi-cellular human liver organoids from pluripotent stem cells. 47 Wendy L. Thompson and Takanori Takebe 1. Introduction. 48 2. Applications of liver organoids.50
VI Contents 3. Overview of differentiation protocol. 51 4. Step-by-step methods.52 5. Technical and design considerations.65 6. Conclusions.66 Acknowledgments.66 References. 66 CHAPTER 4 Pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids. 69 Eleanor Luce and Anne Dubart-Kupperschmitt 1. Introduction. 70 2. Physiology of cholangiocytes. 71 3. Biliary differentiation during development. 74 4. Human cholangiocyte sources for organoids.75 5. Applications of pluripotent stem cell-derived cholangiocytes and cholangiocyte organoids. 76 6. Overview of the protocol. 78 7. Step-by-step methods. 80 8. Conclusion. 89 Acknowledgments.
89 References.90 CHAPTER 5 Differentiation of human airway-organoids from induced pluripotent stem cells (iPSCs). 95 Ruobing Wang, Katie B. McCauley, Darrell N. Kotton, and Finn Hawkins 1. Introduction. 96 2. iPSC-derived airway organoid cell types. 98 3. Applications of airway organoids.99 4. Overview of differentiation protocol. 102 5. Step-by-step methods. 102 6. Conclusion. 110 References.110 CHAPTER 6 A method of generating alveolar organoids using human pluripotent stem cells.115 Yuki Yamamoto, Yohei Korogj, Toyohiro Hirai, and Shimpei Gotoh 1. Introduction. 116 2. Discovery of alveolar organoids. 117
Contents 3. Need of AOs using human ESCs and iPSCs. 118 4. Overview of lung cell differentiation from hPSCs. 118 5. 6. 7. 8. Alveolar organoid cell types.119 Overview of the differentiation protocol.119 Step-by-step methods. 120 Passage of AOs for long-term culture (fibroblast-dependent). 129 9. Differentiation of lung progenitor cells into fibroblast-free (FF) AOs. 131 10. Immunofluorescent analysis of organoids.132 11. The transmission electron microscopic analysis of AT2 cells. 134 12. Technical and design considerations. 136 13. Conclusion. 137 Acknowledgments. 138 References. 138 CHAPTER 7 Generation of small intestinal organoids for experimental intestinal physiology. 143 Meghan Capeling, Sha Huang, Adriana Mulero-Russe, Roberto Cieza, Yu-Hwai Tsai, Andres Garcia, and David R. Hill 1. Introduction. 145 2. Applications of intestinal
organoids. 145 3. Overview of differentiation protocol.146 4. Materials, equipment and reagents. 147 5. Organoid differentiation protocol. 149 6. Application of HIOs, and variations on HIO culture. 159 7. Pros and cons of pluripotent stem cell derived intestinal organoids. 169 8. Troubleshooting and optimization. 169 9. Related techniques.170 10. Ethical considerations and standards. 170 11. Conclusions. 171 References. 171 CHAPTER 8 Pluripotent stem cell derived intestinal organoids with an enteric nervous system.175 Elise Loffet, Lisa Brossard, and Maxime M. Mahe 1. Introduction.176 2. Applications of intestinal organoids with an enteric nervous system.178 vii
Contents 3. Protocol overview.178 4. Step by step methods.180 5. Troubleshooting and optimization. 195 6. Precursor and alternative techniques. 196 7. Summary. 197 Acknowledgments.197 References.197 CHAPTER 9 Generation of human colonic organoids from human pluripotent stem cells. 201 Abdelkader Daoud and Jorge 0. Muñera 1. Introduction. 202 2. Applications of human colonic organoids. 203 3. Overview of HCO differentiation protocol.205 4. Step-by-step protocol.209 5. Statistical analysis.224 6. Pros and cons. 224 7. Troubleshooting and optimization. 225 8. Conclusion.225
References. 226 CHAPTER 10 Single-cell genomic analysis of human cerebral organoids.229 Sabina Kanton, Barbara Treutlein, and J. Gray Camp 1. Introduction.230 2. Overview of the protocol. 232 3. Generating single-cell sequencing data from cerebral organoids.233 4. Basic analysis of organoidscRNA-seq data. 240 5. Conclusions and outlook. 248 Acknowledgments.249 References. 249 Further reading.256 Overview of computational tools for single-cell analysis. 256 Best practices in single-cell RNA-seq analysis. 256 Benchmark batch correction methods. 256 Experimental design to reduce batch effects in single-cell RNA-seq experiments. 256 Trajectory inference benchmark study.256
Contents CHAPTER 11 Generating ventral spinal organoids from human induced pluripotent stem cells.257 Jin-Hui Hor and Shi-Yan Ng 1. Introduction.258 2. Spinal cord development. 259 3. Applications of spinal cord organoids. 263 4. Overview of the differentiation protocol. 265 5. Step-by-step methods.265 6. Technical and design considerations.273 7. Conclusion. 274 Acknowledgments.274 References. 274 CHAPTER 12 Differentiation of retinal organoids from human pluripotent stem cells.279 Clarisse M. Fligor, Kang-Chieh Huang, Sailee S. Lavekar, Kirstin В. VanderWail, and Jason S. Meyer 1. Introduction.280 2. Application of retinal organoids. 281 3. Cell types found within retinal organoids. 284 4. Overview of differentiation
protocol.286 5. Step-by-step methods.287 6. Technical and design considerations.295 7. Conclusions. 298 Acknowledgments.298 References.298 CHAPTER 13 Generation of inner ear organoids from human pluripotent stem cells.303 Jing Nie and Eri Hashino 1. Introduction. 304 2. Overview of the differentiation protocol. 306 3. Applications of inner ear organoids. 306 4. Materials.308 5. Protocol. 312 6. Characterization of inner ear organoids.317 7. Notes.318 8. Safety considerations. 320 Acknowledgments. 320
References.320 IX |
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| spelling | Human pluripotent stem cell derived organoid models edited by Jason R. Spence (Department of Internal Medicine - Gastroenterology, Department of Cell and Developmental Biology, Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, United States) First edition Cambridge, MA ; San Diego, CA Academic Press, an imprint of Elsevier 2020 xiv, 321 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Methods in cell biology Volume 159 Mensch (DE-588)4038639-9 gnd rswk-swf Stammzelle (DE-588)4665329-6 gnd rswk-swf Pluripotenz (DE-588)4420540-5 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Stammzelle (DE-588)4665329-6 s Mensch (DE-588)4038639-9 s Pluripotenz (DE-588)4420540-5 s b DE-604 Spence, Jason R. 1977- (DE-588)1214248314 edt Erscheint auch als Online-Ausgabe 978-0-12-821532-6 Methods in cell biology Volume 159 (DE-604)BV002534878 159 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=032224151&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Human pluripotent stem cell derived organoid models |
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| title_exact_search | Human pluripotent stem cell derived organoid models |
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| title_full | Human pluripotent stem cell derived organoid models edited by Jason R. Spence (Department of Internal Medicine - Gastroenterology, Department of Cell and Developmental Biology, Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, United States) |
| title_fullStr | Human pluripotent stem cell derived organoid models edited by Jason R. Spence (Department of Internal Medicine - Gastroenterology, Department of Cell and Developmental Biology, Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, United States) |
| title_full_unstemmed | Human pluripotent stem cell derived organoid models edited by Jason R. Spence (Department of Internal Medicine - Gastroenterology, Department of Cell and Developmental Biology, Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, United States) |
| title_short | Human pluripotent stem cell derived organoid models |
| title_sort | human pluripotent stem cell derived organoid models |
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