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An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

ABSTRACT: A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.

ORGANISM(S): Dicentrarchus labrax

PROVIDER: GSE85052 | GEO | 2017/02/12

SECONDARY ACCESSION(S): PRJNA336034

REPOSITORIES: GEO

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Project description:Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation, leads to waste and has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as High pressure (HP), are being investigated to prolong shelf-life while assuring high food quality. We applied several tools to evaluate the impacts of HP processing on European sea bass (Dicentrarchus labrax) fillets quality and shelf life. The data here presented includes visual and physical measurements of flesh quality and the microbiome and proteome profiles of control and HP-processed sea bass fillets (600MPa, 25ºC, 5min), after isothermal storage (2°C) for different periods ranging from 1 to 67 days. Color (L-, a- and b- values) change and texture (hardness, cohesiveness and adhesiveness) parameters were obtained by using appropriate colorimeter and texture analyser, respectively, during refrigerated storage. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 16S rRNA gene in five pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. In addition, high-throughput sequencing of the internal transcribed spacer (ITS) region targeting yeast and moulds was run for control or HP-processed fillets at the end of storage (11 or 67 days, respectively), being deposited under SRA accession PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed filets after short (1d) or long-term (11-67 days) storage. These data support the findings reported in “High pressure processing of European sea bass (Dicentrarchus labrax) fillets and tools for flesh quality and shelf life monitoring” (Tsironi et al. 2019).

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An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

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