Ontology highlight
ABSTRACT:
PROVIDER: PRJNA528860 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8776921_1.fastq.gz | Fastqsanger.gz | |||
| SRR8776921_2.fastq.gz | Fastqsanger.gz |
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Project description:Dicentrarchus labrax (European Sea Bass) genome
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Project description:A custom high density oligo-microarray (8 x 15K) was designed and printed by means of the eArray web tool (Agilent) to analyze the transcriptome of the three intestinal sections of Euroipan sea bass (Dicentrarchus labrax). Naïve stock juveniles sea bass, maintained under intensive rearing conditions in the indoor experimental facilities of IATS, were sampled after overnight fasting for anterior, middle and posterior sections of intestine. The array comprised 60-oligomer sequences for 14,147 different sea bass annotated sequences. Total RNA (150ng) from individual fish were labelled with cyanine 3-CTP and 1,000ng of each labelled cRNA were hybridized to microarray slides. Analysis of the scanned data, including principal component analysis and unpaired t-test with Benjamini-Hochberg multiple testing correction, was carried out with GeneSpring GX software (Agilent). Pathway analysis of differentially expressed sequences was performed using the Ingenuity Pathway Analysis (IPA) software.
2017-07-08 | GSE59240 | GEO
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).
2019-11-06 | PXD012737 | Pride
Project description:The European sea bass, Dicentrarchus labrax overview
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Project description:A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from four (4) independent biological replicates, each consisting of pools of five (5) jaws. Statistical analysis with SAM (Significance Analysis of Microarray) identified 333 probes (corresponding to 242 unique transcripts) significantly down-regulated in deformed individuals compared to normal ones. In this study, we analyzed eight(8) samples, four (4) pools of jaws dissected from normal sea bass and four (4) pools of jaws dissected from individuals affected by prognathism. Gene expression profiling was performed using the Agilent-019810 Dicentrarchus labrax Oligo Microarray platform (8 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2010-10-22 | E-GEOD-19001 | biostudies-arrayexpress
Project description:Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.
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Project description:Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.
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Project description: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. Statistical analysis with SAM (Significance Analysis of Microarray) didnât identify any difference in expression patterns between the two groups. Samples were then employed as biological replicates to determine array-to-array reproducibility, the degree of mutual agreement among replicates was estimated using Pearson correlation coefficients on the entire set of expression values. For all pairs of experiments correlation coefficients were always significant (p-value <0.01) and never less than 0.99. In this study, we analyzed six (6) samples, three (3) pools of heads dissected from normal sea bass and three (3) dissected from individuals affected by prognathism. Gene expression profiling was performed using the Agilent-019810 Dicentrarchus labrax Oligo Microarray platform (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
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