The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration.
Dimitri Tolleter, Edward N Smith, Clémence Dupont-Thibert, Clarisse Uwizeye, Denis Vile, Pauline Gloaguen, Denis Falconet, Giovanni Finazzi, Yves Vandenbrouck, Gilles Curien
Author Information
Dimitri Tolleter: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Edward N Smith: Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. ORCID
Clémence Dupont-Thibert: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Clarisse Uwizeye: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Denis Vile: Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), UMR 759, Université de Montpellier, INRAE, Institut Agro, Montpellier, France.
Pauline Gloaguen: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Denis Falconet: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Giovanni Finazzi: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France.
Yves Vandenbrouck: CEA DRF, Gif-sur-Yvette, France.
Gilles Curien: Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France. ORCID
Quantitative analyses and models are required to connect a plant's cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is time-consuming. Consequently, there is a need to centralise the available data and to highlight the remaining knowledge gaps. Here, we present a step-by-step approach to manually extract quantitative data from various information sources, and to unify the data format. First, data from Arabidopsis leaf were collated, checked for consistency and correctness and curated by cross-checking sources. Second, quantitative data were combined by applying calculation rules. They were then integrated into a unique comprehensive, referenced, modifiable and reusable data compendium representing an Arabidopsis reference leaf. This atlas contains the metrics of the 15 cell types found in leaves at the cellular and subcellular levels.
