Investigation Title	Transcription profiling of liver from B6 and 129 mice fed on low and high fat diets	
Comment[Submitted Name]	RAD.Study[study_id=2334]: Low and High Fat Diet on Mice of Two Genetic Backgrounds (B6 vs. 129) - Liver	
Experimental Design	strain_or_line_design	growth_condition_design	transcription profiling by array	
Experimental Design Term Source REF	mo	The MGED Ontology	EFO	
Comment[ArrayExpressReleaseDate]	2007-04-06	
Comment[AEMIAMESCORE]	5	
Comment[ArrayExpressAccession]	E-CBIL-24	
Comment[MAGETAB TimeStamp_Version]	2011-06-28 12:14:24 Last Changed Rev: 14857	
Experimental Factor Name	B6 vs. 129	High-Fat vs. Low-Fat	
Experimental Factor Type	strain_or_line	growth_condition	
Experimental Factor Term Source REF	
Person Last Name	Kahn	Liu	
Person First Name	Ronald	Junmin	
Person Mid Initials	
Person Email	c.ronald.kahn@joslin.harvard.edu	junmin@pcbi.upenn.edu	
Person Phone	
Person Fax	
Person Address	1 Joslin Place; Boston; Massachusetts; 02215; USA	
Person Affiliation	Joslin Diabetes Center and Harvard Medical School	
Person Roles	submitter	data_coder	
Person Roles Term Source REF			
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2007-04-06	
PubMed ID	15855315	
Publication DOI	15855315	
Publication Author List	Biddinger Sudha B, Almind Katrine, Miyazaki Makoto, Kokkotou Efi, Ntambi James M, Kahn C Ronald	
Publication Title	Effects of diet and genetic background on sterol regulatory element-binding protein-1c, stearoyl-CoA desaturase 1, and the development of the metabolic syndrome.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Both environmental and genetic factors play important roles in the development of the metabolic syndrome. To elucidate how these factors interact under normal conditions, C57Bl/6 (B6) and 129S6/SvEvTac (129) mice were placed on a low-fat or high-fat diet.  Liver samples were extracted and hybridized to Affymetrix Genome U74 (version 2) arrays.	
Protocol Name	cbil.upenn.edu:RAD.Protocol:4732:Protocol	cbil.upenn.edu:RAD.Protocol:4731:Protocol	cbil.upenn.edu:RAD.Protocol:3547:Protocol	cbil.upenn.edu:RAD.Protocol:925:Protocol	cbil.upenn.edu:RAD.Protocol:263:Protocol	cbil.upenn.edu:RAD.Protocol:284:Protocol	
Protocol Type	grow	grow	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	The HFD derives 55% calories from fat, 21% calories protein, and 24% calories from carbohydrates and was found to contain 4.2% saturated fatty acids, 5.0% MUFAs, and 11.2% polyunsaturated fatty acids. The LFD and HFD have 15.4 and 7.1 mg cholesterol per 100 g, respectively. Arachidonic acid was undetectable. The mice were maintained on a 12-h light-dark cycle; unless otherwise indicated, serum samples were taken and mice were killed between 9:00 and 11:00 A.M., in the nonfasted state at 6 months of age. Insulin levels were measured in plasma samples of random fed mice using the Crystal Chem ELISA kit and mouse insulin standards. Three independent cohorts were used to perform these experiments.	The LFD derives 14% calories from fat, 25% calories from protein, and 61% calories from carbohydrates and was found to contain 1.5% saturated fatty acids, 2.7% monounsaturated fatty acids (MUFAs), and 0.6% polyunsaturated fatty acids by weight.  Arachidonic acid was undetectable. The mice were maintained on a 12-h light-dark cycle; unless otherwise indicated, serum samples were taken and mice were killed between 9:00 and 11:00 A.M., in the nonfasted state at 6 months of age. Insulin levels were measured in plasma samples of random fed mice using the Crystal Chem ELISA kit and mouse insulin standards. Three independent cohorts were used to perform these experiments.	The RNeasy procedure represents a novel technology for RNA isolation. This technology combines the selective binding properties of a silica-gel-based membrane with the speed of microspin technology. A specialized high-salt buffer system allows RNA to bind to the RNeasy silica-gel membrane. Biological samples are first lysed and homogenized in the presence of a highly denaturing guanidine isothiocyanate (GITC)-containing buffer, which immediately inactivates RNases to ensure isolation of intact RNA. Ethanol is added to provide appropriate binding conditions, and the sample is then applied to an RNeasy column where the total RNA binds to the membrane and contaminants are efficiently washed away. High-quality RNA is then eluted in water.	See pages 2.1.10-2.1.17 of the GeneChip Expression Analysis Technical Manual for all details. First-strand cDNA is synthesized from (5.0 to 20.0 ug) high-quality total RNA, using the GeneChip T7-Oligo(dT) Promoter Primer Kit or random primers provided with the SuperScript Choice Kit. Second-strand synthesis is carried out in: 1X second-strand reaction buffer, 200 uM each dNTP mix, 10 U E. coli DNA ligase, 40 U E. coli DNA polymerase I, 2 U E. coli RNase H in a final volume of 150 uL. The double-stranded cDNA is cleaned-up using the components supplied with the GeneChip Sample Cleanup Module. Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, P/N 900182) is used to synthesize biotin-labeled cRNA target. The latter is cleaned up using the components supplied with the GeneChip Sample Cleanup Module.	The fragmented cRNA is mixed with the hybridization cocktail, and heat shocked at 99C for 5 minutes.  In the meanwhile, the probe array is filled with hybridization buffer and incubated at 45C for 10 minutes with rotation.  The heated hybridization cocktail is then transferred to a 45C heat block for 5 minutes, and spun at maximum speed in a microcentrifuge for 5 minutes.  Fill the probe array cartridge with the clarified hybridization cocktail and place probe array in rotisserie box in 45C oven. Hybridize for 16 hours.	An absolute expression analysis examines the cell intensity file (*.CEL) from one experiment. For each transcript represented on the probe array, the expression algorithm computes the 1) detection call [present, absent, or marginal (unable to call the transcript present or absent), or no call]; 2) detection p-value; 3) signal (background subtracted and adjusted for noise); 4) stat pairs; 5) stat pairs used. The expression values are saved in the .CHP file.	
Protocol Parameters						TGT;	
Protocol Hardware					Affymetrix Fluidics Station 400	
Protocol Software						Affymetrix MAS 5.0 Absolute Expression Analysis	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	
SDRF File	E-CBIL-24.sdrf.txt	
Term Source Name	ncbitax	The MGED Ontology	mgd	nci_meta		cbil_cv	ArrayExpress	mo	The MGED Ontology	EFO	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.informatics.jax.org/	http://ncimeta.nci.nih.gov/indexMetaphrase.html		http://www.cbil.upenn.edu/anatomy.php3	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version