Title Page
Abstract
Contents
Chapter 1. Introduction 8
1.1. Human Lung Airway 8
1.2. Differentiation of human lung airway cells 20
1.3. Organoids 28
1.4. Single Cell RNA sequencing 40
1.5. Epithelial cell response to SARS-CoV-2 virus 48
1.6. Purpose of this study 56
Chapter 2. Materials and Methods 59
2.1. Human tissue samples 59
2.2. Human primary distal airway organoids 59
2.3. Air-liquid interface (ALI) culture of organoids 60
2.4. scRNA-seq of in vitro human primary airway cultures 61
2.5. Immunofluorescent staining of 2D ALI and 3D cultures 62
2.6. Quantitative PCR 63
2.7. Virus preparation 64
2.8. Viral infection procedure 64
2.9. Transmission electron microscopy (TEM) 65
2.10. K-chip genotyping array 65
2.11. scRNA-seq data analysis 66
2.12. Cell cycle scoring 66
2.13. Integration of OSCA and tissue scRNA-seq data 67
2.14. Cell type annotation prediction using CellTypist 67
2.15. Rare cell score 67
2.16. Rare cell population lineage trajectory 68
2.17. Single cell multiome data analysis 68
2.18. Identification of expression profiles 69
2.19. scRNA-seq data analysis with virus-infected samples 70
Chapter 3. Body 71
3.1. Archiving human airway organoids 71
3.2. Single-cell atlas of cellular diversity in airway cells 74
3.3. Single-cell multiomics of rare airway lineages 79
3.4. Immune response signatures in lung tissues 83
3.5. Airway organoid responses to viral infections 88
Chapter 4. Conclusion 94
Abstract 100
Bibliography 102