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Article Dans Une Revue Plant and Cell Physiology Année : 2021

MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

Résumé

Abstract Although RNA sequencing (RNAseq) has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such a tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labeling and organization of samples to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas, as a very valuable and complementary resource.
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supplemental data set1_RNAseq-data.xlsx (105.04 Ko) Télécharger le fichier
supplemental data set2_GeneChip-data.xlsx (13.95 Ko) Télécharger le fichier
supplemental data set3_software-API-UI.xlsx (10.6 Ko) Télécharger le fichier
supplemental table 1_reference-genomes.xlsx (8.7 Ko) Télécharger le fichier
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hal-03420304 , version 1 (22-11-2021)

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Sebastien Carrere, Jerome Verdier, Pascal Gamas. MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula. Plant and Cell Physiology, 2021, 62 (9), pp.1494-1500. ⟨10.1093/pcp/pcab110⟩. ⟨hal-03420304⟩
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