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Title: Molecular pathology of the ARF induced by choline deficiency and of the protection afforded by fish oil      
dateReleased:
12-06-2011
description:
Weanling rats fed a choline-deficient diet develop acute renal failure (ARF) after 6-7 days of receiving the experimental diet. Its pathogenesis is controversial. Menhaden oil has a protective effect in this experimental model. The aim of this study is to describe both the genetic profile and its changes when vegetable oils are replaced by menhaden oil. Wistar, weanling rats from the Animal Facility of the Centre of Experimental and Applied Pathology were divided into 4 groups and fed with the following diets: 1- Choline-deficient diet with vegetable oils as lipids (corn and hydrogenated oils); 2- Choline-supplemented diet with vegetable oils as lipids; 3- Choline-deficient diet with menhaden oil as lipid; and 4- Choline supplemented diet with menhaden oil as lipid. Animals were sacrificed after 6 days of receiving the experimental diets. The right kidney was cryopreserved. In this assay biological duplicated samples were used. In order to evaluate changes in gene expression WT Expression Kit (Ambion, USA) over the platform GeneChip® Gene 1.0 ST Rat Genome Array (Affymetrix Inc, USA) was used. Fluorescent distribution in the array was obtained using the language R (www-r-project.org), in house own algorithms and other formsbioconductor tools . We analyzed the differential gene expression, using as cut value p<0.01 with fdr control & |log FC|>1.5, in all groups. Rats fed with diets 2, 3 and 4 have similar genetic profiles. However, the comparison between rats fed with diets 2 and 4 showed 35 genes with diferential expression. As these rats did not have renal necrosis, we can hypothesize that the differential expression is due to the menhaden oil of the diet. In short, the massive analysis of genetic expression allowed to confirm that menhaden oil has a protective effect in this experimental model and to identify 35 genes that could be responsible of that protection. Twenty eight animals were sacrificed after 6 days of receiving the experimental diets. The right kidney was cryopreserved for microarray analysis. Cryopreserved kidney was pulverized under liquid-nitrogen conditions. Total RNA was purified from 30 mg of frozen rat kidney tissue. Each sample represents a pool of 3 animals (except CD+AM SN with 2 animals/pool), to reduce biological variation. In this assay biological duplicated samples were used.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-34139
refinement:
raw
alternateIdentifiers:
34139
keywords:
functional genomics
dateModified:
12-12-2011
availability:
available
types:
gene expression
name:
Rattus norvegicus
ID:
A-GEOD-6247
name:
[RaGene-1_0-st] Affymetrix Rat Gene 1.0 ST Array
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-34139/E-GEOD-34139.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-34139/E-GEOD-34139.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34139
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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