ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"NCBITAXON"	"XCO"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/XCO"	
Term Source Version	"78"	"111"	"20"	"2"	"33"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Experimental Conditions Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-23742"
Study Title	"Gene expression profiling of mouse liver during a diet of fish oil or olive oil with or without indomethacin. [original title: Gene expression data from mouse liver]"
Study Description	"We used microarray analysis to examine which genes are differentially expressed in mice that received a combination of fish oil and indomethacin. We fed low density lipoprotein receptor knock-out (LDLR-/-) mice with 6% of olive oil (control) or fish oil diets in the presence or absence of indomethacin for 12 weeks. We collected total RNA from liver samples and pooled 6 RNA samples in each group for Affymetrix microarrays."
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Study Public Release Date	"2012-11-06"
Study File Name	"s_E-GEOD-23742_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"22847176"
Study Publication DOI	"10.1194/jlr.M029843"
Study Publication Author List	"Murali G, Milne GL, Webb CD, Stewart AB, McMillan RP, Lyle BC, Hulver MW, Saraswathi V"
Study Publication Title	"Fish oil and indomethacin in combination potently reduce dyslipidemia and hepatic steatosis in LDLR(-/-) mice."
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STUDY FACTORS
Study Factor Name	"organism"	"diet"	"drug"
Study Factor Type	"organism"	"diet"	"drug"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-23742_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE23742-2"	"P-GSE23742-3"	"P-GSE23742-4"	"P-GSE23742-5"	"P-GSE23742-6"	"P-GSE23742-7"	"P-GSE23742-1"
Study Protocol Type	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"	"feature_extraction"	"bioassay_data_transformation"
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Study Protocol Description	"LDLR-/- mice were fed a high fat diet supplemented with 6% olive oil or fish oil in the presence or absence of indomethacin for 12 weeks. Olive oil and fish oil were mixed with diet whereas indomethacin (6mg/liter) was administered in drinking water."	"Trizol extraction of total RNA was performed according to the manufacturer's instructions. We pooled 6 RNA samples in each group for the microarray experiment."	"Affymetrix WT Sense reactions, using the Affymetrix WT Sense reaction kit (catalog#900652)"	"The targets in hybridization cocktail were heat denatured at 99°C for 5 minutes, cooled to 45°C for 5 minutes, centrifuged and then loaded on the Affymetrix cartridge arrays for a hybridization period of 16 hours at 45°C, with rotation of 60 RPM in Affymetrix Model 645 Hybridization Oven"	"GeneChips were scanned using Affymetrix 7G plus scanner."	"The data were analyzed with GCOS software and by using Affymetrix default analysis settings and RMA as normalization method, signal intensity values are calculated"	"ID_REF =  VALUE = RMA Signal Intensity"
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STUDY CONTACTS
Study Person Last Name	"Saraswathi"	"Viswanathan"
Study Person First Name	"Viswanathan"	"Saraswathi"
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Study Person Email	"geo@ncbi.nlm.nih.gov"	""
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Study Person Address	"Vanderbilt University, 702 Light Hall, 23rd Ave and Pierce, Nashville, TN, USA"	""
Study Person Affiliation	"Vanderbilt University"	""
Study Person Roles	"submitter"	""
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