Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Hongjie Li, Jasper Janssens, Maxime De Waegeneer, Sai Saroja Kolluru, Kristofer Davie, Vincent Gardeux, Wouter Saelens, Fabrice David, Maria Brbić, Katina I. Spanier, Jure Leskovec, Colleen N. McLaughlin, Qijing Xie, Robert C. Jones, Katja Brueckner, Jiwon Shim, Sudhir Gopal Tattikota, Frank Schnorrer, Katja Rust, Todd Nystul, Zita Carvalho-Santos, Carlos Ribeiro, Soumitra Pal, Sharvani Mahadevaraju, Teresa M. Przytycka, Aaron M. Allen, Stephen F. Goodwin, Cameron W. Berry, Margaret T. Fuller, Helen White‐Cooper, Erika Matunis, Stephen DiNardo, Anthony Galenza, Lucy Erin O’Brien, Julian A. T. Dow, Heinrich Jasper, Brian Oliver, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts, Devika Agarwal, Yasir H. Ahmed-Braimah, Michelle N Arbeitman, Majd Ariss, Jordan Augsburger, Kumar Ayush, Catherine C. Baker, Torsten U. Banisch, Katja Birker, Rolf Bodmer, Benjamin Bolival, Susanna E. Brantley, Julie A. Brill, Nora C. Brown, Norene A. Buehner, Xiaoyu Cai, Rita Cardoso-Figueiredo, Fernando Casares, Amy K. Chang, Thomas R. Clandinin, Sheela Crasta, Claude Desplan, Angela M. Detweiler, Darshan B. Dhakan, Erika Doná, Stefanie Engert, Swann Floc’hlay, Nancy George, Amanda J. González-Segarra, Andrew K. Groves, Samantha C. Gumbin, Yanmeng Guo, D. Harris, Yael Heifetz, Stephen L Holtz, Felix Horns, Bruno Hudry, Ruei‐Jiun Hung, Yuh Nung Jan, Jacob S Jaszczak, Gregory S.X.E. Jefferis, Jim Karkanias, Timothy L. Karr, Nadja Sandra Katheder, James Kezos, Anna Kim, Seung K. Kim, Lutz Kockel, Νικόλαος Κωνσταντινίδης, Thomas B. Kornberg, Henry M. Krause, Andrew Thomas Labott, Meghan Laturney, Ruth Lehmann, Sarah G. Leinwand, Jun Li, Joshua Shing Shun Li, Kai Li
Abstract
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.