Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly-Reference-Cited by-同舟云学术

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

Published:2022-03-04 Issue:6584 Volume:375 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Li Hongjie¹²³^ORCID,Janssens Jasper⁴⁵^ORCID,De Waegeneer Maxime⁴⁵^ORCID,Kolluru Sai Saroja⁶⁷⁸,Davie Kristofer⁴^ORCID,Gardeux Vincent⁹¹⁰^ORCID,Saelens Wouter⁹¹⁰^ORCID,David Fabrice P. A.⁹¹⁰¹¹^ORCID,Brbić Maria⁸¹²^ORCID,Spanier Katina⁴⁵^ORCID,Leskovec Jure⁸¹²^ORCID,McLaughlin Colleen N.¹^ORCID,Xie Qijing¹^ORCID,Jones Robert C.⁶⁷⁸^ORCID,Brueckner Katja¹³,Shim Jiwon¹⁴^ORCID,Tattikota Sudhir Gopal¹⁵¹⁶^ORCID,Schnorrer Frank¹⁷^ORCID,Rust Katja¹⁸¹⁹^ORCID,Nystul Todd G.¹⁹^ORCID,Carvalho-Santos Zita²⁰^ORCID,Ribeiro Carlos²⁰^ORCID,Pal Soumitra²¹^ORCID,Mahadevaraju Sharvani²²^ORCID,Przytycka Teresa M.²¹^ORCID,Allen Aaron M.²³^ORCID,Goodwin Stephen F.²³^ORCID,Berry Cameron W.²⁴^ORCID,Fuller Margaret T.²⁴^ORCID,White-Cooper Helen²⁵^ORCID,Matunis Erika L.²⁶^ORCID,DiNardo Stephen²⁷²⁸^ORCID,Galenza Anthony²⁹^ORCID,O’Brien Lucy Erin²⁹,Dow Julian A. T.³⁰^ORCID,Jasper Heinrich³¹,Oliver Brian²²^ORCID,Perrimon Norbert¹⁵¹⁶^ORCID,Deplancke Bart⁹¹⁰^ORCID,Quake Stephen R.⁶⁷⁸^ORCID,Luo Liqun¹^ORCID,Aerts Stein⁴⁵^ORCID,Agarwal Devika³²,Ahmed-Braimah Yasir³³,Arbeitman Michelle³⁴,Ariss Majd M.³⁵,Augsburger Jordan¹³,Ayush Kumar¹²,Baker Catherine C.³⁶,Banisch Torsten³⁷,Birker Katja³⁸,Bodmer Rolf³⁸,Bolival Benjamin³⁶,Brantley Susanna E.³⁶,Brill Julie A.³⁹⁴⁰,Brown Nora C.⁴¹,Buehner Norene A.⁴¹,Cai Xiaoyu Tracy³¹,Cardoso-Figueiredo Rita²⁰,Casares Fernando⁴²,Chang Amy⁴³,Clandinin Thomas R.⁴⁴,Crasta Sheela⁶⁷⁸,Desplan Claude⁴⁵,Detweiler Angela M.⁸,Dhakan Darshan B.²⁰,Donà Erika⁴⁶,Engert Stefanie⁴³,Floc’hlay Swann⁴⁵,George Nancy⁴⁷,González-Segarra Amanda J.⁴³,Groves Andrew K.³⁴⁸,Gumbin Samantha²⁹,Guo Yanmeng⁴⁹⁵⁰,Harris Devon E.³⁶,Heifetz Yael⁵¹,Holtz Stephen L.⁵²,Horns Felix⁵³,Hudry Bruno⁵⁴,Hung Ruei-Jiun¹⁵,Jan Yuh Nung⁴⁹⁵⁰,Jaszczak Jacob S.⁴⁹⁵⁰,Jefferis Gregory S. X. E.⁴⁶,Karkanias Jim⁸,Karr Timothy L.⁵⁵,Katheder Nadja Sandra³¹,Kezos James³⁸,Kim Anna A.²⁹⁵⁶⁵⁷,Kim Seung K.²⁴⁵⁸,Kockel Lutz²⁴,Konstantinides Nikolaos⁵⁹,Kornberg Thomas B.⁶⁰,Krause Henry M.⁶¹,Labott Andrew Thomas²⁹,Laturney Meghan⁴³,Lehmann Ruth⁶²,Leinwand Sarah⁴³,Li Jiefu¹,Li Joshua Shing Shun¹⁵,Li Kai⁴⁹⁵⁰,Li Ke⁴⁹⁵⁰,Li Liying⁴⁹⁵⁰,Li Tun⁴⁹⁵⁰,Litovchenko Maria⁹¹⁰,Liu Han-Hsuan⁴⁹⁵⁰,Liu Yifang¹⁵,Lu Tzu-Chiao²,Manning Jonathan⁴⁷,Mase Anjeli¹³,Matera-Vatnick Mikaela⁴¹,Matias Neuza Reis³⁶,McDonough-Goldstein Caitlin E.⁶³⁶⁴,McGeever Aaron⁸,McLachlan Alex D.⁶⁵,Moreno-Roman Paola²⁹,Neff Norma⁸,Neville Megan²³,Ngo Sang²⁹,Nielsen Tanja³⁸,O’Brien Caitlin E.⁴⁹⁵⁰,Osumi-Sutherland David⁶⁶,Özel Mehmet Neset⁶⁷,Papatheodorou Irene⁴⁷,Petkovic Maja⁴⁹⁵⁰,Pilgrim Clare⁶⁸,Pisco Angela Oliveira⁸,Reisenman Carolina⁴³,Sanders Erin Nicole²⁹,dos Santos Gilberto⁶⁹,Scott Kristin⁴³,Sherlekar Aparna²⁹,Shiu Philip⁴³,Sims David³²,Sit Rene V.⁸,Slaidina Maija⁷⁰,Smith Harold E.⁷¹,Sterne Gabriella⁴³,Su Yu-Han²⁹,Sutton Daniel⁷²,Tamayo Marco³⁸,Tan Michelle⁸,Tastekin Ibrahim²⁰,Treiber Christoph⁷³,Vacek David¹,Vogler Georg³⁸,Waddell Scott⁷³,Wang Wanpeng⁶⁰,Wilson Rachel I.⁵²,Wolfner Mariana F.⁴¹,Wong Yiu-Cheung E.³⁶,Xie Anthony¹,Xu Jun¹⁵,Yamamoto Shinya³⁷⁴,Yan Jia⁸,Yao Zepeng⁴³,Yoda Kazuki²⁹,Zhu Ruijun⁴⁹⁵⁰,Zinzen Robert P.⁷⁵,

Affiliation:

1. Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA.

2. Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA.

3. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

4. VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven 3000, Belgium.

5. Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.

6. Department of Bioengineering, Stanford University, Stanford, CA, USA.

7. Department of Applied Physics, Stanford University, Stanford, CA, USA.

8. Chan Zuckerberg Biohub, San Francisco CA, USA.

9. Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

10. Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.

11. Bioinformatics Competence Center, EPFL, Switzerland.

12. Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

13. Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA.

14. Department of Life Science, College of Natural Science, Hanyang University, 04763 Seoul, Republic of Korea.

15. Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.

16. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.

17. Aix-Marseille University, CNRS, IBDM (UMR 7288), Turing Centre for Living Systems, 13009 Marseille, France.

18. Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps-University, Marburg, Germany.

19. Department of Anatomy, University of California, San Francisco, CA 94143, USA.

20. Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal.

21. National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

22. Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

23. Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, UK.

24. Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

25. Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UK.

26. Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

27. Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.

28. The Penn Institute for Regenerative Medicine, Philadelphia, PA 19104, USA.

29. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.

30. Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.

31. Immunology Discovery, Genentech, Inc., South San Francisco, CA 94080, USA.

32. MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.

33. Department of Biology, Syracuse University, Syracuse, NY 13244 USA.

34. Biomedical Sciences Department, Florida State University, Tallahassee, FL, USA.

35. Department of Genetics, Harvard Medical School, Boston, MA, USA.

36. Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

37. Skirball Institute and HHMI, New York University Langone Medical Center, New York City, NY 10016, USA.

38. Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.

39. Cell Biology Program, The Hospital for Sick Children (SickKids), Toronto, ON M5G 0A4, Canada.

40. Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.

41. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

42. CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain.

43. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

44. Department of Neurobiology, Stanford University, Stanford, CA 94305, USA.

45. Department of Biology, New York University, New York, New York 10003, USA.

46. Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

47. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

48. Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.

49. Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.

50. Howard Hughes Medical Institute, San Francisco, CA, USA.

51. The Hebrew University of Jerusalem, Jerusalem, Israel.

52. Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

53. Department of Bioengineering and Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA.

54. Université Côte d’Azur, CNRS, INSERM, iBV, France.

55. Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA.

56. University of California, Santa Barbara, CA 93106, USA.

57. Uppsala University, Sweden.

58. Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.

59. Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France.

60. Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA.

61. Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.

62. Skirball Institute, Department of Cell Biology and HHMI, New York University Langone Medical Center, New York City, NY 10016.

63. Department of Biology, Syracuse University, Syracuse, NY, USA.

64. Department of Evolutionary Biology, University of Vienna, Vienna, Austria.

65. Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.

66. European Bioinformatics Institute (EMBL/EBI), Wellcome Trust Genome Campus, Cambridge, UK.

67. Department of Biology, New York University, New York, NY 10003, USA.

68. Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK.

69. The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

70. Skirball Institute, Faculty of Medicine, New York University, New York, NY 10016.

71. Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA.

72. Graduate Program in Genetics and Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.

73. Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3TA, UK.

74. Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA.

75. Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference58 articles.

1. Sex Limited Inheritance in Drosophila

2. The Genome Sequence of Drosophila melanogaster

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4. FlyMine: an integrated database for Drosophila and Anopheles genomics

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