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Journal Articles Science Year : 2022

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

Hongjie Li (1) , Jasper Janssens , Maxime de Waegeneer , Sai Saroja Kolluru , Kristofer Davie , Vincent Gardeux , Wouter Saelens , Fabrice David , Maria Brbić , Katina Spanier , Jure Leskovec , Colleen Mclaughlin , Qijing Xie , Robert Jones , Katja Brueckner , Jiwon Shim , Sudhir Gopal Tattikota , Frank Schnorrer (2) , Katja Rust , Todd Nystul , Zita Carvalho-Santos , Carlos Ribeiro , Soumitra Pal , Sharvani Mahadevaraju , Teresa Przytycka , Aaron Allen , Stephen Goodwin , Cameron Berry , Margaret Fuller , Helen White-Cooper , Erika Matunis , Stephen Dinardo , Anthony Galenza , Lucy Erin O’brien , Julian Dow , Heinrich Jasper , Brian Oliver , Norbert Perrimon , Bart Deplancke , Stephen Quake , Liqun Luo , Stein Aerts , Devika Agarwal , Yasir Ahmed-Braimah , Michelle Arbeitman , Majd Ariss , Jordan Augsburger , Kumar Ayush , Catherine Baker , Torsten Banisch , Katja Birker , Rolf Bodmer , Benjamin Bolival , Susanna Brantley , Julie Brill , Nora Brown , Norene Buehner , Xiaoyu Tracy Cai , Rita Cardoso-Figueiredo , Fernando Casares , Amy Chang , Thomas Clandinin , Sheela Crasta , Claude Desplan , Angela Detweiler , Darshan Dhakan , Erika Donà , Stefanie Engert , Swann Floc’hlay , Nancy George , Amanda González-Segarra , Andrew Groves , Samantha Gumbin , Yanmeng Guo , Devon Harris , Yael Heifetz , Stephen Holtz , Felix Horns , Bruno Hudry , Ruei-Jiun Hung , Yuh Nung Jan , Jacob Jaszczak , Gregory Jefferis , Jim Karkanias , Timothy Karr , Nadja Sandra Katheder , James Kezos , Anna Kim , Seung Kim , Lutz Kockel , Nikolaos Konstantinides , Thomas Kornberg , Henry Krause , Andrew Thomas Labott , Meghan Laturney , Ruth Lehmann , Sarah Leinwand , Jiefu Li , Joshua Shing Shun Li , Kai Li , Ke Li , Liying Li , Tun Li , Maria Litovchenko , Han-Hsuan Liu , Yifang Liu , Tzu-Chiao Lu , Jonathan Manning , Anjeli Mase , Mikaela Matera-Vatnick , Neuza Reis Matias , Caitlin Mcdonough-Goldstein , Aaron Mcgeever , Alex Mclachlan , Paola Moreno-Roman , Norma Neff , Megan Neville , Sang Ngo , Tanja Nielsen , Caitlin O’brien , David Osumi-Sutherland , Mehmet Neset Özel , Irene Papatheodorou , Maja Petkovic , Clare Pilgrim , Angela Oliveira Pisco , Carolina Reisenman , Erin Nicole Sanders , Gilberto dos Santos , Kristin Scott , Aparna Sherlekar , Philip Shiu , David Sims , Rene Sit , Maija Slaidina , Harold Smith , Gabriella Sterne , Yu-Han Su , Daniel Sutton , Marco Tamayo , Michelle Tan , Ibrahim Tastekin , Christoph Treiber , David Vacek , Georg Vogler , Scott Waddell , Wanpeng Wang , Rachel Wilson , Mariana Wolfner , Yiu-Cheung Wong , Anthony Xie , Jun Xu , Shinya Yamamoto , Jia Yan , Zepeng Yao , Kazuki Yoda , Ruijun Zhu , Robert Zinzen
Jasper Janssens
Maxime de Waegeneer
Sai Saroja Kolluru
  • Function : Author
Kristofer Davie
Vincent Gardeux
Wouter Saelens
Fabrice David
Maria Brbić
Katina Spanier
Jure Leskovec
Colleen Mclaughlin
Qijing Xie
Robert Jones
Katja Brueckner
  • Function : Author
Jiwon Shim
Sudhir Gopal Tattikota
Katja Rust
Todd Nystul
Zita Carvalho-Santos
Carlos Ribeiro
Soumitra Pal
Sharvani Mahadevaraju
Teresa Przytycka
Aaron Allen
Stephen Goodwin
Cameron Berry
Margaret Fuller
Helen White-Cooper
Erika Matunis
Stephen Dinardo
Anthony Galenza
Lucy Erin O’brien
  • Function : Author
Julian Dow
Heinrich Jasper
  • Function : Author
Brian Oliver
Norbert Perrimon
Bart Deplancke
Stephen Quake
Liqun Luo
Stein Aerts
Devika Agarwal
  • Function : Author
Yasir Ahmed-Braimah
  • Function : Author
Michelle Arbeitman
  • Function : Author
Majd Ariss
  • Function : Author
Jordan Augsburger
  • Function : Author
Kumar Ayush
  • Function : Author
Catherine Baker
  • Function : Author
Torsten Banisch
  • Function : Author
Katja Birker
  • Function : Author
Rolf Bodmer
  • Function : Author
Benjamin Bolival
  • Function : Author
Susanna Brantley
  • Function : Author
Julie Brill
  • Function : Author
Nora Brown
  • Function : Author
Norene Buehner
  • Function : Author
Xiaoyu Tracy Cai
  • Function : Author
Rita Cardoso-Figueiredo
  • Function : Author
Fernando Casares
  • Function : Author
Amy Chang
  • Function : Author
Thomas Clandinin
  • Function : Author
Sheela Crasta
  • Function : Author
Claude Desplan
  • Function : Author
Angela Detweiler
  • Function : Author
Darshan Dhakan
  • Function : Author
Erika Donà
  • Function : Author
Stefanie Engert
  • Function : Author
Swann Floc’hlay
  • Function : Author
Nancy George
  • Function : Author
Amanda González-Segarra
  • Function : Author
Andrew Groves
  • Function : Author
Samantha Gumbin
  • Function : Author
Yanmeng Guo
  • Function : Author
Devon Harris
  • Function : Author
Yael Heifetz
  • Function : Author
Stephen Holtz
  • Function : Author
Felix Horns
  • Function : Author
Bruno Hudry
  • Function : Author
Ruei-Jiun Hung
  • Function : Author
Yuh Nung Jan
  • Function : Author
Jacob Jaszczak
  • Function : Author
Gregory Jefferis
  • Function : Author
Jim Karkanias
  • Function : Author
Timothy Karr
  • Function : Author
Nadja Sandra Katheder
  • Function : Author
James Kezos
  • Function : Author
Anna Kim
  • Function : Author
Seung Kim
  • Function : Author
Lutz Kockel
  • Function : Author
Nikolaos Konstantinides
Thomas Kornberg
  • Function : Author
Henry Krause
  • Function : Author
Andrew Thomas Labott
  • Function : Author
Meghan Laturney
  • Function : Author
Ruth Lehmann
  • Function : Author
Sarah Leinwand
  • Function : Author
Jiefu Li
  • Function : Author
Joshua Shing Shun Li
  • Function : Author
Kai Li
  • Function : Author
Ke Li
  • Function : Author
Liying Li
  • Function : Author
Tun Li
  • Function : Author
Maria Litovchenko
  • Function : Author
Han-Hsuan Liu
  • Function : Author
Yifang Liu
  • Function : Author
Tzu-Chiao Lu
  • Function : Author
Jonathan Manning
  • Function : Author
Anjeli Mase
  • Function : Author
Mikaela Matera-Vatnick
  • Function : Author
Neuza Reis Matias
  • Function : Author
Caitlin Mcdonough-Goldstein
  • Function : Author
Aaron Mcgeever
  • Function : Author
Alex Mclachlan
  • Function : Author
Paola Moreno-Roman
  • Function : Author
Norma Neff
  • Function : Author
Megan Neville
  • Function : Author
Sang Ngo
  • Function : Author
Tanja Nielsen
  • Function : Author
Caitlin O’brien
  • Function : Author
David Osumi-Sutherland
  • Function : Author
Mehmet Neset Özel
  • Function : Author
Irene Papatheodorou
  • Function : Author
Maja Petkovic
  • Function : Author
Clare Pilgrim
  • Function : Author
Angela Oliveira Pisco
  • Function : Author
Carolina Reisenman
  • Function : Author
Erin Nicole Sanders
  • Function : Author
Gilberto dos Santos
  • Function : Author
Kristin Scott
  • Function : Author
Aparna Sherlekar
  • Function : Author
Philip Shiu
  • Function : Author
David Sims
  • Function : Author
Rene Sit
  • Function : Author
Maija Slaidina
  • Function : Author
Harold Smith
  • Function : Author
Gabriella Sterne
  • Function : Author
Yu-Han Su
  • Function : Author
Daniel Sutton
  • Function : Author
Marco Tamayo
  • Function : Author
Michelle Tan
  • Function : Author
Ibrahim Tastekin
  • Function : Author
Christoph Treiber
  • Function : Author
David Vacek
  • Function : Author
Georg Vogler
  • Function : Author
Scott Waddell
  • Function : Author
Wanpeng Wang
  • Function : Author
Rachel Wilson
  • Function : Author
Mariana Wolfner
  • Function : Author
Yiu-Cheung Wong
  • Function : Author
Anthony Xie
  • Function : Author
Jun Xu
  • Function : Author
Shinya Yamamoto
  • Function : Author
Jia Yan
  • Function : Author
Zepeng Yao
  • Function : Author
Kazuki Yoda
  • Function : Author
Ruijun Zhu
  • Function : Author
Robert Zinzen
  • Function : Author

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.
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Dates and versions

hal-03795698 , version 1 (17-10-2022)

Identifiers

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Hongjie Li, Jasper Janssens, Maxime de Waegeneer, Sai Saroja Kolluru, Kristofer Davie, et al.. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science, 2022, 375 (6584), ⟨10.1126/science.abk2432⟩. ⟨hal-03795698⟩
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