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Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

ABSTRACT: In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) was used to compare expression profiles of mineralization-induced VSa13 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change.

ORGANISM(S): Sparus aurata

PROVIDER: GSE18915 | GEO | 2011/06/01

SECONDARY ACCESSION(S): PRJNA121267

REPOSITORIES: GEO

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Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls

2011-06-01 | GSE18941 | GEO

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

Project description:In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) was used to compare expression profiles of mineralization-induced VSa13 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa13 cell cultures and three (3) collected from mineralization-induced VSa13 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (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 that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2011-06-01 | E-GEOD-18915 | biostudies-arrayexpress

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls

Project description:In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GEO accession: GPL6467) was used to compare expression profiles of mineralization-induced VSa16 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa16 cell cultures and three (3) collected from mineralization-induced VSa16 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (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 that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2011-06-01 | E-GEOD-18941 | biostudies-arrayexpress

Phytogenics from sage and lemon verbena promote innate immunity and barrier function in the gut of gilthead seabream (Sparus aurata)

Project description:Deciphering the dietary immunomodulatory effects of a medicinal plant leaf extract (MPLE) obateined from sage (Salvia officinalis, Lamiaceae) and lemon verbena (Lippia citriodora, Verbenaceae) upon the gut-associated lymphoid tissue (GALT) of gilthead seabream (Sparus aurata).

2021-06-02 | GSE166558 | GEO

Comparative gel-based proteomics analysis to disclose the impact of different stressors on gilthead seabream liver

Project description:Hepatic metabolic adjustments are key adaptive mechanisms to stress in fish targeting at increasing energy availability for the animal to efficiently cope with a stressor. A comparative gel-based proteomics analysis (2D-DIGE) was employed to discover the set of liver proteins involved in the adaptive processes that tune the physiological response to chronic stressors in Sparus aurata. Three separated trials were established where fish were submitted to different stressors (overcrowding, net handling and hypoxia). Two intensities for each stressor were tested, in triplicate tanks. Two liver samples per tank (6 per experimental treatment) were collected for liver proteome analysis at the end of each trial.

2021-04-22 | PXD024804 | Pride

Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

2013-01-03 | GSE32501 | GEO

Transcriptome analysis of gilthead sea bream (Sparus aurata) brain after exposure to environmental concentrations of human pharmaceuticals

Project description:A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals.

2014-05-22 | GSE38195 | GEO

Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

Project description:Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression. [1] Pombinho, A.R., LaizM-CM-), V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406. Sparus aurata oligo-DNA microarray (GPL6467) was used to compare gene expression profiles between Control (WT) and FHL2-transfected (F2) VSa16 cell lines. Gene expression profiles of both WT and F2 cells were assessed either at T0 (initial confluent cultures) or T4 (4 weeks of cell confluency). Four (4) pools of cells were taken from both WT and F2 groups at each time point and stored in RNA later at -20M-BM-0C until RNA extraction.

2013-01-03 | E-GEOD-32501 | biostudies-arrayexpress

Genome expression profile of early response to photobacteriosis in gilthead sea bream (Sparus aurata)

Project description:Analysis of the gene expression profiles of Sparus aurata head kidney after infection with Photobaterium damselae piscicida. The expression levels of 21,497 sea bream transcripts, on both directions, 24 and 48 hours post-infection, were compared with the levels detected in uninfected individuals.

2013-02-22 | GSE26651 | GEO

Transcriptomic response of skeletal muscle to lipopolysaccharide in the gilthead seabream (Sparus aurata)

Project description:The physiological consequences of an activation of the immune system in fish are not well understood. In particular, skeletal muscle, due to its essential role in locomotion and whole-animal energy homeostasis, is a potentially important target of inflammation. In this study, we have evaluated the in vivo effects of lipopolysaccharide (LPS) on the white and red skeletal muscle transcriptome of the gilthead seabream (Sparus aurata) by microarray analysis at 24 and 72 hours after injection. In white muscle, the transcriptomic response was characterized by an up-regulation of genes involved in carbohydrate catabolism and protein synthesis at 24 hours and a complete reversal of this pattern at 72 hours. In red muscle, an up-regulation of genes involved in carbohydrate catabolism and protein synthesis was observed only at 72 hours after LPS administration. Interestingly, both white and red muscles showed a similar consistent down-regulation of immune genes at 72 hours post-injection. However, genes involved in muscle contraction showed a general up-regulation in response to LPS in both types of muscle. In summary, LPS administration causes muscle type-specific responses regarding the expression of genes involved in carbohydrate and protein metabolism and a common decreased expression of immune genes in skeletal muscle, concomitant with increased expression of genes for contractile elements. Our results evidence a robust and tissue-specific transcriptomic response of the skeletal muscle to an acute inflammatory challenge.

2012-03-16 | GSE36339 | GEO

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