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Analysis of gene expression profiles on 38 days-old sea bass heads

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. Statistical analysis with SAM (Significance Analysis of Microarray) didn’t 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.

ORGANISM(S): Dicentrarchus labrax

PROVIDER: GSE19041 | GEO | 2010/10/22

SECONDARY ACCESSION(S): PRJNA120529

REPOSITORIES: GEO

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Analysis of gene expression profiles on 38 days-old sea bass heads

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.

2010-10-22 | E-GEOD-19041 | biostudies-arrayexpress

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

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Comparison of gene expression profile between 58 days-old prognatous sea bass jaws and control ones

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

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Comparison of gene expression profile between 58 days-old prognatous sea bass jaws and control ones

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

Study of the onset of puberty in the European sea bass

Project description:Pubertal development in males starts with the onset of spermatogenesis that implies the division of primary spermatogonia and their subsequent entry into meiosis. Whole genome microarray expression profile was used as a means to explore the molecular basis underlying the onset of pubertal development in sea bass. The present study is aimed at the characterization of the expression of genes involved in the onset of spermatogenesis in the European sea bass. The study is focused on the first stages of the process including the appearance of spermatocytes and thus the first meiotic divisions. The transcriptomic study using a sea bass-specific microarray resulted in a number of genes differentially expressed during the onset of spermatogenesis. Among those, genes involved in cell-cycle progression, microtubule assembly during meiosis or retinoic acid signaling pathway indicating that they can be used as potential molecular markers for the onset of spermatogenesis in sea bass.

2017-06-23 | GSE47400 | GEO

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2017-07-20 | GSE101662 | GEO

The Gene expression gradient through the intestine tract of European Sea Bass (Dicentrarchus labrax)

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

Effects of the total replacement of fish meal and fish oil with plant protein and oil sources on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) sub-families exhibiting different growth potentials on an all plant-based diet

Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families.

2011-09-01 | GSE27649 | GEO

Transcriptional analysis on the effect of the overexpression of VvSUC11,VvSUC12,or VvSUC27 in tomato on the growth of fruit

Project description:Purpose: We used transcriptome sequencing to study the regulated mechanism of VvSUC11,VvSUC12,or VvSUC27 on tomato fruit growth. Methods: the 35S:: VvSUC11, VvSUC12, and VvSUC27 constructs were introduced into transgenic tomatoes (Micro-Tom) by the Agrobacterium-mediated transformation, 5 DPA (days after anthesis) fruit was collected, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data. Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to over 40 million clean reads obtained from sequencing were mapped on the reference genome of Solanum lycopersicum. High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (1> R2 > 0.99, P < 0.001) , reflecting the robustness of our library preparation from tomato RNA samples. Compared with WT lines, there were 2459 DEGs in the VvSUC11-overexpressing lines, of which 1283 genes were upregulated and 1176 genes were downregulated. Whereas, there were 1369 DEGs in VvSUC12-overexpressing lines, including 544 upregulated and 825 downregulated genes. In the meanwhile,there were 1777 DEGs in VvSUC27-overexpressing lines, including 623 upregulated and 1154 downregulated genes.

2020-11-16 | GSE161505 | GEO

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