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Transcriptomic and proteomic data in developing tomato fruit

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBELOUAH, Isma
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBÉNARD, Camille
hal.structure.identifierBioEcon Sci Ctr, Inst Bot & Mol Genet
dc.contributor.authorDENTON, Alisandra
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorBLEIN-NICOLAS, Melisande
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorBALLIAU, Thierry
hal.structure.identifierEcophysiologie et Génomique Fonctionnelle de la Vigne [UMR EGFV]
dc.contributor.authorTEYSSIER, Emeline
hal.structure.identifierEcophysiologie et Génomique Fonctionnelle de la Vigne [UMR EGFV]
dc.contributor.authorGALLUSCI, Philippe
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [ GeT-PlaGe]
dc.contributor.authorBOUCHEZ, Olivier
hal.structure.identifierBioEcon Sci Ctr, Inst Bot & Mol Genet
dc.contributor.authorUSADEL, Björn
hal.structure.identifierGénétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon]
dc.contributor.authorZIVY, Michel
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGIBON, Yves
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCOLOMBIE, Sophie
dc.date.issued2020-02
dc.identifier.issn2352-3409
dc.description.abstractEnTranscriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure. From 34,725 possible transcripts identified in the tomato, 22,877 were quantified in at least one of the nine developmental stages. For the proteome analysis, label-free liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used. Peptide ions, and subsequently the proteins from which they were derived, were quantified by integrating the signal intensities obtained from extracted ion currents (XIC) with the MassChroQ software. Absolute concentrations of individual proteins were estimated for 2375 proteins by using a mixed effects model from log10-transformed intensities and normalized to the total protein content. Transcriptomics data are available via GEO repository with accession number GSE128739. The raw MS output files and identification data were deposited on-line using the PROTICdb database (http://moulon.inra.fr/protic/tomato_fruit_development) and MS proteomics data have also been deposited to the ProteomeXchange with the dataset identifier PXD012877. The main added value of these quantitative datasets is their use in a mathematical model to estimate protein turnover in developing tomato fruit.
dc.language.isoen
dc.publisherElsevier
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enProteomics
dc.subject.enTranscriptomics
dc.subject.enTomato fruit development
dc.subject.enPericarp
dc.subject.enTime-series
dc.subject.enAbsolute quantification
dc.subject.enProtein turnover
dc.title.enTranscriptomic and proteomic data in developing tomato fruit
dc.typeArticle de revue
dc.typeData paper
dc.identifier.doi10.1016/j.dib.2019.105015
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalData in Brief
bordeaux.page1-8
bordeaux.volume28
bordeaux.peerReviewedoui
hal.identifierhal-02539392
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02539392v1
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