Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression in the Atlantic salmon adipose-derived stromal-vascular fraction during differentiation into adipocytes

ABSTRACT: Changes of gene expression in primary cell cultures of salmon adipose-derived stromal-vascular fraction were studied at six time-points that covered the key differentiation events: confluence, clonal expansion, determination and establishment of the mature adipocyte phenotype. Time-course experiment: six developmental stages of stromal-vascular fraction against the pooled reference. Biological replicates: 5 per developmental stage, pooled samples of all 6 stages were used as common reference. One stage per array.

ORGANISM(S): Salmo salar

SUBMITTER: Aleksei Krasnov

PROVIDER: E-GEOD-18389 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression profiles in Atlantic salmon adipose-derived stromo-vascular fraction during differentiation into adipocytes.

Todorcević Marijana M Skugor Stanko S Krasnov Aleksei A Ruyter Bente B

BMC genomics 20100117

<h4>Background</h4>Excessive fat deposition is one of the largest problems faced by salmon aquaculture industries, leading to production losses due to high volume of adipose tissue offal. In addition, increased lipid accumulation may impose considerable stress on adipocytes leading to adipocyte activation and production and secretion of inflammatory mediators, as observed in mammals.<h4>Results</h4>Microarray and qPCR analyses were performed to follow transcriptome changes during adipogenesis in ...[more]

PMID: 20078893

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Project description:Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs) was constucted. The viral microarrays wereused to classify the majority of SGIV transcripts into three temporal kinetic classes (immediate-early, IE; early, E; late, L) during an in vitro infection by their dependence on de novo protein synthesis inhibitor and viral DNA replication. Keywords: drug response To map the SGIV transcripts into temporal kinetic classes during the infection in vitro, GS cells were treated with drug inhibitors as previously described with some slight modifications. Briefly, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with either CHX or PAA, which inhibited de novo protein synthesis and viral DNA replication mechanisms, respectively. To distinguish between viral IE transcripts and other transcripts, cells infected with SGIV (MOI of 5) or mock infected were treated with CHX (100 Âµg/ml), and then harvested at 8 h p.i. Whereas, viral E and L transcripts were categorized when cells infected with SGIV (MOI of 5) in the presence and absence of PAA (200 Âµg/ml), respectively. Until at 36 h p.i., cells were collected for RNA extraction. In a comparison analysis, we used Significance Analysis of Microarrays (SAM) software to identify the groups of different expression genes between the drug-treated samples and untreated samples. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Significance is based on an estimated of FDRâ¤5% and a 2 fold-change cutoff. Only the genes that met the following three criteria could be categorized into various temporal kinetic classes: (i) a viral gene was considered to be a IE transcript if its expression level increased or weakly affected under CHX treatment, (ii) a viral gene was considered to be a L transcript if its median intensity ratio in the PAA-treated samples was at least two-fold lower than that in the untreated samples and (iii) a viral gene was considered to be a E transcript if it expressed higher or remained within the two- fold range after PAA treatment but was inhibited distinctly by CHX treatment. To identify the significant differences in gene expression, a criterion with at least two-fold change combined with studentâs one sample t-test p value <0.05 was adopted.

Dataset Information

Gene expression in the Atlantic salmon adipose-derived stromal-vascular fraction during differentiation into adipocytes

Publications

Gene expression profiles in Atlantic salmon adipose-derived stromo-vascular fraction during differentiation into adipocytes.

Similar Datasets

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