Mus musculus
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ABSTRACT:
PROVIDER: PRJNA184410 | ENA |
REPOSITORIES: ENA
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Project description:High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis. Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet. Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.
2008-12-10 | E-GEOD-10493 | biostudies-arrayexpress
Project description:High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis. Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects
2008-12-10 | GSE10493 | GEO
Project description:The C57BL/6J mouse model develops obesity and pre-diabetes when fed a high-fat diet. In this experiment, DNA methylation was assessed globally at specific CpG sites in liver tissue from mice receiving high-fat diet (45E% from fat) for 13 weeks (Control) or high-fat diet supplemented with 20% (w/w) of freeze-dried lingonberries (n=4). Our findings show that lingonberries prevent development of high-fat induced obesity, hepatic steatosis and low-grade inflammation, and the DNA was hypermethylated in mice receiving lingonberries compared to control. Genome wide hepatic DNA methylation comparison between mice fed high-fat diet with or without a lingonberry supplement (n=4/group).
2015-09-20 | E-GEOD-67277 | biostudies-arrayexpress
Project description:Several studies have described phenotypic changes in offspring of mice exposed to environmental factors including diet, but the effect of diet on sperm chromatin remains unclear. We used a high fat diet (HFD) induced obesity mouse model, and examined chromatin of paternal spermatozoa. We performed chromatin immunoprecipitation followed by high throughput sequencing using specific H3 antibodies or specific H3K4me1antibodies.
2015-08-20 | GSE72211 | GEO
Project description:One of the metabolic consequences of obesity is abnormal lipid accumulation in the liver, or hepatosteatosis, which can develop intomore serious diseases in the non-alcoholic liver disease (NAFLD) spectrum including non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma. Therefore, it is necessary to understand the metabolic changes that occur in hepatosteatosisin order toprevent disease progression.The liver plays a major role in regulating macronutrient and energy homeostasis in both the fed and fasted states. However, whether hepatosteatosis influences thepostprandial molecularresponse, specifically to dietary fat,has not been investigated.Therefore, the goal of this study was to comparethe proteome and phosphoproteome of steatotic livers from diet-induced obese (DIO) mice and control livers from lean mice in the postprandial response to dietary fat. Using untargeted LC-MS/MS analysis, we identified significant alterations in the levels of proteins involved in macronutrient and energy metabolism in livers of DIO compared to lean mice. In addition, uniquely phosphorylated proteins in livers of DIO andlean mice reflect regulatory mechanisms controlling cellular processes contributingto hepatosteatosis. Theresultsof this studyexpandourknowledge ofthe metabolic consequences that occur duringhepatosteatosisandtheinfluence of dietary fat on NAFLD progression.
2020-06-19 | MSV000085612 | MassIVE
