Applying Single Cell RNA-seq to Dissect a Phenotype

Recent technological advances in single cell RNA-sequencing (scRNA-seq) have enabled the study of complex cellular dynamics, including the identification of accurate transcriptomic gene signatures in a multitude cell types. Its superior resolution has facilitated the discovery of novel sub-cell types, biomarkers, and intricate cellular differentiation processes which were undetectable using formerly conventional techniques such as RNA-seq. In this thesis, I employ scRNA-seq to create two comprehensive cell atlases of the Drosophila developing eye and glia during the late third instar larval stage. After resolving the cellular heterogeneity and dynamics that characterize wild type eye tissues, I subjected Rbf (Retinoblastoma-family protein) mutant eyes and Amalgam (Ama) depleted brains to scRNA-seq in order to identify the cellular transcriptomic perturbations in their respective contexts. These findings led to the discovery of novel players in the Retinoblastoma and Receptor Tyrosine Kinase (RTK) pathways. Finally, my analysis of the aforementioned mutant and knockdown phenotypes demonstrates the benefits of scRNA-seq and emphasizes its value in uncovering the molecular mechanisms that drive cellular transcriptomic discrepancies.