Grones, Carolin; Eekhout, Thomas; Shi, Dongbo; Neumann, Manuel; Berg, Lea S; Ke, Yuji; Shahan, Rachel; Cox, Kevin L; Gomez-Cano, Fabio; Nelissen, Hilde; Lohmann, Jan U; Giacomello, Stefania; Martin, Olivier C; Cole, Benjamin; Wang, Jia-Wei; Kaufmann, Kerstin; Raissig, Michael T; Palfalvi, Gergo; Greb, Thomas; Libault, Marc; ... (2024). Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. The Plant Cell, 36(4), pp. 812-828. American Society of Plant Biologists 10.1093/plcell/koae003
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Single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) 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 datasets 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.
Item Type: |
Journal Article (Further Contribution) |
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Division/Institute: |
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Development 08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) |
UniBE Contributor: |
Berg, Lea Sophie, Raissig, Michael Thomas |
Subjects: |
500 Science > 580 Plants (Botany) |
ISSN: |
1040-4651 |
Publisher: |
American Society of Plant Biologists |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
18 Jan 2024 10:32 |
Last Modified: |
30 Mar 2024 00:14 |
Publisher DOI: |
10.1093/plcell/koae003 |
PubMed ID: |
38231860 |
BORIS DOI: |
10.48350/191752 |
URI: |
https://boris.unibe.ch/id/eprint/191752 |
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