Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

Author:

Grones Carolin12,Eekhout Thomas123ORCID,Shi Dongbo45,Neumann Manuel6ORCID,Berg Lea S7ORCID,Ke Yuji12,Shahan Rachel89ORCID,Cox Kevin L10ORCID,Gomez-Cano Fabio11,Nelissen Hilde12ORCID,Lohmann Jan U4ORCID,Giacomello Stefania12,Martin Olivier C13ORCID,Cole Benjamin14ORCID,Wang Jia-Wei15ORCID,Kaufmann Kerstin6ORCID,Raissig Michael T7ORCID,Palfalvi Gergo16,Greb Thomas4ORCID,Libault Marc17ORCID,De Rybel Bert12ORCID

Affiliation:

1. Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052 , Belgium

2. VIB Centre for Plant Systems Biology , Ghent 9052 , Belgium

3. VIB Single Cell Core Facility, Ghent 9052, Belgium

4. Centre for Organismal Studies, Heidelberg University , 69120 Heidelberg , Germany

5. Institute of Biochemistry and Biology, University of Potsdam , 14476 Potsdam , Germany

6. Institute of Biology, Humboldt-Universität zu Berlin , 10115 Berlin , Germany

7. Institute of Plant Sciences, University of Bern , 3012 Bern , Switzerland

8. Department of Biology, Duke University , Durham, NC 27708 , USA

9. Howard Hughes Medical Institute, Duke University , Durham, NC 27708 , USA

10. Donald Danforth Plant Science Center , St. Louis, MO 63132 , USA

11. Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, MI 48109 , USA

12. SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology , 17165 Solna , Sweden

13. Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay , Gif-sur-Yvette 91192 , France

14. DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA

15. National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS) , Shanghai 200032 , China

16. Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research , 50829 Cologne , Germany

17. Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia , Columbia, MO 65201 , USA

Abstract

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

Funder

European Research Council

ERC StG TORPEDO

ERC CoG PIPELINES

ERC CoG PLANTSTEMS

ERC SyG

Flemish Government VLAIO

VIB TechWatch Funding

EMBO YIP

Nebraska Soybean Board

National Science Foundation

USDA-NIFA

Nebraska Research Initiative

DFG FOR5235

US National Institutes of Health

U.S. Department of Energy Joint Genome Institute

Office of Science of the U.S. Department of Energy

French State

Saclay Plant Sciences

National Natural Science Foundation of China

Chinese Academy of Sciences

Japan Science and Technology Agency

Deutsche Forschungsgemeinschaft

DFG projects

Publisher

Oxford University Press (OUP)

Subject

Cell Biology,Plant Science

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