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

For more than 100 years, the fruit fly <i>Drosophila melanogaster</i> has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula <i>Drosophilae</i>, 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 <i>Drosophila</i> community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.