TY - JOUR
T1 - Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics
AU - Grones, Carolin
AU - Eekhout, Thomas
AU - Shi, Dongbo
AU - Neumann, Manuel
AU - Berg, Lea S.
AU - Ke, Yuji
AU - Shahan, Rachel
AU - Cox, Kevin L.
AU - Gomez-Cano, Fabio
AU - Nelissen, Hilde
AU - Lohmann, Jan U.
AU - Giacomello, Stefania
AU - Martin, Olivier C.
AU - Cole, Benjamin
AU - Wang, Jia Wei
AU - Kaufmann, Kerstin
AU - Raissig, Michael T.
AU - Palfalvi, Gergo
AU - Greb, Thomas
AU - Libault, Marc
AU - De Rybel, Bert
N1 - Publisher Copyright:
© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.
PY - 2024/4
Y1 - 2024/4
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85187579079&partnerID=8YFLogxK
U2 - 10.1093/plcell/koae003
DO - 10.1093/plcell/koae003
M3 - Review article
C2 - 38231860
AN - SCOPUS:85187579079
SN - 1040-4651
VL - 36
SP - 812
EP - 828
JO - Plant Cell
JF - Plant Cell
IS - 4
ER -