Abstract
The ability to obtain single cell transcriptomes for stable cell types and dynamic cell states is ushering in a new era for biology. We created the Tabula Drosophilae, a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body. Over 100 researchers from the fly community contributed annotations to >250 distinct cell types across all tissues. 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 that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
FCA Consortium
Overall coordination
Hongjie Li, Jasper Janssens, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts
Logistical coordination
Hongjie Li, Jasper Janssens, Maxime De Waegeneer, Sai Saroja Kolluru, Robert C. Jones, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts
Biohub: Aaron McGeever, Angela Oliveira Pisco, Jim Karkanias, Sheela Crasta
Flybase: Gil dos Santos, Clare Pilgrim, Alex McLachlan
EBI: David Osumi-Sutherland, Irene Papatheodorou, Nancy George, Jonathan Manning
Tissue dissection
Liqun Luo lab (head, body, antenna, haltere): Liqun Luo, Hongjie Li, Jiefu Li, David Vacek, Anthony Xie
Lucy O’Brien lab (gut): Lucy Erin O’Brien, Yu-Han Su, Erin Nicole Sanders, Samantha Gumbin, Paola Moreno-Roman, Aparna Sherlekar, Andrew Thomas Labott, Sang Ngo
Norbert Perrimon lab (Malpighian tubule): Norbert Perrimon, Ruei-Jiun Hung, Jun Xu
Yuh-Nung Jan lab (body wall): Yuh Nung Jan, Jacob S. Jaszczak, Ruijun Zhu, Ke Li, Yanmeng Guo, Kai Li, Liying Li, Tun Li, Han-Hsuan Liu, Caitlin E. O’Brien, Wanpeng Wang, Maja Petkovic
Rolf Bodmer lab (heart): Rolf Bodmer, Georg Vogler, Marco Tamayo, James Kezos, Katja Birker, Tanja Nielsen
Mariana Wolfner lab (male reproductive glands): Mariana F. Wolfner, Norene A. Buehner
Kristin Scott lab (leg, wing, proboscis & max palp), Kristin Scott, Amy Chang, Stefanie Engert, Amanda Gonzalez, Meghan Laturney, Sarah Leinwand, Carolina Reisenman, Philip Shiu, Gabriella Sterne, Zepeng Yao
Heinrich Jasper lab (fat body, oenocyte): Heinrich Jasper, Xiaoyu Tracy Cai, Nadja Sandra Katheder
Tom Kornberg lab (trachea): Thomas B Kornberg, Wanpeng Wang
Margaret Fuller lab (testis): Margaret T. Fuller, Neuza Reis Matias, Cameron W. Berry, Susanna E. Brantley, Catherine C. Baker, Devon E. Harris, Yiu-Cheung E. Wong, Benjamin Bolival
Todd Nystul lab (ovary): Todd G. Nystul, Katja Rust
Katja Brueckner lab (hemocyte): Katja Brueckner, Jordan Augsburger, Anjeli Mase
Seung Kim lab (insulin-producing cell, corpora cardiaca cell): Seung K. Kim, Lutz Kockel
Library preparation and sequencing
Luo and Quake labs: Hongjie Li, Sai Saroja Kolluru, Colleen N. McLaughlin, Qijing Xie, Robert C. Jones, Felix Horns
Biohub: Angela M. Detweiler, Jia Yan, Michelle Tan, Norma Neff, Rene V. Sit
NIH group: Harold E. Smith, Brian Oliver
Data analysis
Jasper Janssens, Maxime De Waegeneer, Kristofer Davie, Swann Floc’hlay, Stein Aerts, Vincent Gardeux, Wouter Saelens, Fabrice David, Maria Litovchenko, Bart Deplancke, Maria Brbić, Kumar Ayush, Hongjie Li, Jure Leskovec
Case study analysis/writing
Common cell - hemocyte: Katja Brueckner, Jiwon Shim, Sudhir Tattikota, Jasper Janssens, Hongjie Li
Common cell - muscle: Frank Schnorrer, Jasper Janssens
Gut data integration: Wouter Saelens
Metabolic pathway: Carlos Ribeiro, Zita Carvalho-Santos, Darshan B. Dhakan, Rita Cardoso-Figueiredo,
Ovary data integration: Katja Rust, Todd G. Nystul
Sex differences: Brian Oliver, Soumitra Pal, Teresa Przytycka, Aaron M. Allen, Devika Agarwal, Stephen F Goodwin, Julian A. T. Dow
Testis annotation & trajectory: Margaret T. Fuller, Cameron W. Berry, Erika L. Matunis, Stephen DiNardo, Helen White-Cooper, Brian Oliver, Sharvani Mahadevaraju, Julie A. Brill, Henry M. Krause, Wouter Saelens, Bart Deplancke
Cell type annotation
SCope team: Stein Aerts (PI), Jasper Janssens, Maxime De Waegeneer, Kristofer Davie
ASAP team: Bart Deplancke (PI), Vincent Gardeux, Wouter Saelens, Fabrice David
Gut: Lucy Erin O’Brien, Anthony Galenza, Aparna Sherlekar, Erin Nicole Sanders, Yu-Han Su, Anna A. Kim, Kazuki Yoda, Norbert Perrimon, Joshua Shing Shun Li
Malpighian tubule: Norbert Perrimon, Julian A. T. Dow, Jun Xu, Jasper Janssens, Yifang Liu
Body wall: Yuh Nung Jan, Jacob S. Jaszczak, Ruijun Zhu, Ke Li, Yanmeng Guo, Liying Li, Hongjie Li
Heart: Rolf Bodmer, Georg Vogler, Hongjie Li, Jasper Janssens
Muscle: Frank Schnorrer, Jasper Janssens
Male reproductive glands: Mariana F. Wolfner, Nora C. Brown, Yasir Ahmed-Braimah, Helen White-Cooper, Mikaela Matera-Vatnick, Timothy L. Karr
Leg, wing, prob. and max palp: Kristin Scott, Zepeng Yao, Carlos Ribeiro, Ibrahim Tastekin
Antenna and haltere, Liqun Luo, Hongjie Li, Colleen N. McLaughlin, Andrew K. Groves, Shinya Yamamoto, Daniel Sutton, Rachel I. Wilson, Stephen L. Holtz
Fatbody and oenocyte: Heinrich Jasper, Xiaoyu Tracy Cai, Nadja Sandra Katheder, Sudhir Gopal Tattikota, Carlos Ribeiro, Zita Carvalho-Santos, Rita Cardoso-Figueiredo, Hongjie Li, Jasper Janssens Trachea: Thomas B Kornberg, Wanpeng Wang, Hongjie Li
Testis (see case study)
Ovary: Todd G. Nystul, Katja Rust, Ruth Lehman, Maija Slaidina, Torsten Banisch, Zita Carvalho-Santos, Mariana F. Wolfner, Wanpeng Wang, Brian Oliver, Sharvani Mahadevaraju
Hemocyte, Katja Brueckner, Jiwon Shim, Sudhir Gopal Tattikota, Jasper Janssens, Hongjie Li
Insulin-producing cell (IPC) and corpora cardiaca cell (CC): Seung K. Kim, Lutz Kockel, Maria Brbić
Head and body: Aaron M. Allen, Bruno Hudry, Caitlin E. McDonough-Goldstein, Christoph Treiber, Clare Pilgrim, Claude Desplan, David Sims, Devika Agarwal, Erika Donà, Fernando Casares, Gregory S.X.E. Jefferis, Majd M. Ariss, Megan Neville, Michelle Arbeitman, Mehmet Neset Özel, Nikolaos Konstantinides, Scott Waddell, Stephen F Goodwin, Thomas R. Clandinin, Yael Heifetz, Jasper Janssens, Hongjie Li, Stein Aerts
Writing group
Hongjie Li, Jasper Janssens, Norbert Perrimon, Bart Deplancke, Stephen R. Quake, Liqun Luo, Stein Aerts
Principal investigators (A-Z):
Stein Aerts, Yasir Ahmed-Braimah, Rolf Bodmer, Julie A. Brill, Katja Brueckner, Fernando Casares, Thomas R. Clandinin, Bart Deplancke, Claude Desplan, Stephen DiNardo, Julian A. T. Dow, Margaret T. Fuller, Stephen F Goodwin, Andrew K. Groves, Yael Heifetz, Bruno Hudry, Yuh Nung Jan, Heinrich Jasper, Gregory S.X.E. Jefferis, Timothy L. Karr, Seung K. Kim, Nikolaos Konstantinides, Thomas B Kornberg, Henry M. Krause, Jure Leskovec, Hongjie Li, Liqun Luo, Erika L. Matunis, Todd G. Nystul, Lucy Erin O’Brien, Brian Oliver, Norbert Perrimon, Teresa M Przytycka, Stephen R. Quake, Carlos Ribeiro, Katja Rust, Frank Schnorrer, Kristin Scott, Jiwon Shim, Helen White-Cooper, Rachel I. Wilson, Mariana F. Wolfner, Shinya Yamamoto