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Liver mRNA microarray study for mice treated with various diets

ABSTRACT: The goal of this study was to investigate the effects of vairous diets on the expression of genes involved in intermediary metabolism in liver. Adult wild type male mice (3 for each group) were fed with the corresponding diet for two weeks, and then liver samples were collected. Total RNA was isolated by the RNAzol B reagent, and pellet was disolved in DEPC-treated water. Total RNA was isolated using RNA Bee reagent (Tel-Test Inc., Friendswood, TX) per the manufacturers protocol. RNA concentrations were quantified using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) at a wavelength of 260 nm. The integrity of the total RNA samples was evaluated by formaldehyde-agarose gel electrophoresis, and confirmed by visualization of 18S and 28S rRNA bands. The gene expression was determined by Affymetrix Mouse 430 2.0 Gene Expression Microarray. Nine different diets were used: Diet 1. TD.84224. EFA Deficient diet; Diet 2. TD 97070. High fat diet: Diet 3. TD.88137. Adjusted Calories Diet (42% from fat) (Western Diet); Diet 4. TD.02028. Atherogenic Rodent Diet; Diet 5. TD.89247. 60% Fructose Diet; Diet 6. TD.94048. AIN-93M Purified Diet, Diet 7. Current rodent diet used in LAR; Diet 8. DHA-supplemented diet; Diet 9. Diet-restriction: 75% of the diet consumed by ad lib feeding. Mice (n=3/diet) were fed one of these diets (Harlan Laboratories) for 3 weeks. All mice were euthanized in the morning (8:00–10:00 A.M.) and blood and tissue samples were collected. All procedures were approved in accordance with Institutional Animal Care and Use Committee guidelines.

ORGANISM(S): Mus musculus

PROVIDER: GSE51885 | GEO | 2014/02/24

SECONDARY ACCESSION(S): PRJNA225676

REPOSITORIES: GEO

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Liver mRNA microarray study for mice treated with various diets

Project description:The goal of this study was to investigate the effects of vairous diets on the expression of genes involved in intermediary metabolism in liver. Adult wild type male mice (3 for each group) were fed with the corresponding diet for two weeks, and then liver samples were collected. Total RNA was isolated by the RNAzol B reagent, and pellet was disolved in DEPC-treated water. Total RNA was isolated using RNA Bee reagent (Tel-Test Inc., Friendswood, TX) per the manufacturers protocol. RNA concentrations were quantified using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) at a wavelength of 260 nm. The integrity of the total RNA samples was evaluated by formaldehyde-agarose gel electrophoresis, and confirmed by visualization of 18S and 28S rRNA bands. The gene expression was determined by Affymetrix Mouse 430 2.0 Gene Expression Microarray. Nine different diets were used: Diet 1. TD.84224. EFA Deficient diet; Diet 2. TD 97070. High fat diet: Diet 3. TD.88137. Adjusted Calories Diet (42% from fat) (Western Diet); Diet 4. TD.02028. Atherogenic Rodent Diet; Diet 5. TD.89247. 60% Fructose Diet; Diet 6. TD.94048. AIN-93M Purified Diet, Diet 7. Current rodent diet used in LAR; Diet 8. DHA-supplemented diet; Diet 9. Diet-restriction: 75% of the diet consumed by ad lib feeding. Mice (n=3/diet) were fed one of these diets (Harlan Laboratories) for 3 weeks. All mice were euthanized in the morning (8:00‚Äì10:00 A.M.) and blood and tissue samples were collected. All procedures were approved in accordance with Institutional Animal Care and Use Committee guidelines. A total of 27 samples were analyzed, n=3 per diet, control: AIN-93 Purified Diet

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Hepatic gene expression in wild type and SHPKO mice fed chow or western diet

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Project description:Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments. Distal colon tissues from Sprague Dawley rats fed a variety of diets (see summary) were removed from RNAlater stabilisation reagent (Sigma, Australia) they had been stored in,, placed in 1 ml of TRIzol® Reagent (Invitrogen, Australia) and homogenised usingbeads (mix of 2.5 mm glass and 0.1 - 1.0 mm diameter silicon-zirconian beads) in a MiniBeadbeater-8 (BioSpec Products Inc., USA). Total RNA was extracted (using TRIzol® Reagent manufacturer's instructions) and further purified using RNAeasy mini spin columns (QIAGEN, Australia) with a DNase on-column digestion as per manufacturer's instructions.RNA integrity was checked using a Bioanalyzer 2100 (Agilent Technologies, USA) andquantified using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). RNA samples with insufficinet quality and quantity were not assayed. The numbers of rats arrayed from each diet were as follows: CON, 5;LAMS, 7; HAMS, 8; HAMSB, 9; LAW, 6; HAW , 8. This gives a total of 43 arrays.

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