Generation and characterization of the sea bass Dicentrarchus labrax brain and liver transcriptomes |
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| Authors: | Elodie Magnanou,Christophe Klopp,Celine Noirot,Laurence Besseau,Jack Falcó n |
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| Affiliation: | 1. Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, BIOM, Observatoire Océanologique, F-66650, Banyuls/Mer, France;2. CNRS, UMR7232, BIOM, Avenue Fontaulé, 66650 Banyuls‐sur‐Mer, France;3. INRA, Plateforme bioinformatique Toulouse Midi-Pyrénées, UR875 Biométrie et Intelligence Artificielle, BP 52627, 31326 Castanet-Tolosan Cedex, France |
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| Abstract: | The sea bass Dicentrarchus labrax is the center of interest of an increasing number of basic or applied research investigations, even though few genomic or transcriptomic data is available. Current public data only represent a very partial view of its transcriptome. To fill this need, we characterized brain and liver transcriptomes in a generalist manner that would benefit the entire scientific community. We also tackled some bioinformatics questions, related to the effect of RNA fragment size on the assembly quality. |
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| Keywords: | BBH, Bidirectional Best Hit bp, base pair BWA, Burrows&ndash Wheeler Aligner CDK, Cyclin Dependent Kinase CNRS, Centre National de la Recherche Scientifique EMBOSS, European Molecular Biology Open Software Suite ENCODE, ENCyclopedia Of DNA Elements EST, Expressed Sequence Tag FAO, Food and Agriculture Organization of the United Nations FL, fork length GDR, Groupement De Recherche GnRH, Gonadotropin-Releasing Hormone GSI, Gonado-Somatic Index GO, Gene Ontology IFREMER, Institut Franç ais de Recherche pour l'Exploitation de la Mer IGBMC, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire KAAS, KEGG Automatic Annotation Server KEGG, Kyoto Encyclopedia of Genes and Genomes KO, KEGG Orthology ORF, Open Reading Frame PCR, Polymerase Chain Reaction SD, standard deviation SEM, standard error of the mean SNP, single nucleotide polymorphism TGICL, TIGR Gene Indices Clustering Tools TIGR, The Institute for Genomic Research UPMC, Université Pierre et Marie Curie WEGO, Web Gene Ontology Annotation Plotting |
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