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

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution