Comment[ArrayExpressAccession]	E-GEOD-31947
MAGE-TAB Version	1.1						
Public Release Date	2013-03-22
Investigation Title	Profiling aorta from high fat diet (HFD)-fed ApoE KO and wild type C57BL6 mice						
Comment[Submitted Name]	Profiling aorta from high fat diet (HFD)-fed ApoE KO and wild type C57BL6 mice
Experiment Description	This program aimed to understand gene expression changes in aorta during atherosclerotic lesion progression with an objective to identify genes that may present new opportunities for drug intervention The HFD-fed ApoE KO mice aorta profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in comparison to the HFD-fed WT C57BL6 controls.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Wang	Wang	Zhang				
Person First Name	I-Ming	I-Ming	Bin				
Person Email	i_ming_wang@merck.com						
Person Affiliation	Merck Research Lab						
Person Phone	215-652-1287						
Person Fax	215-993-1835						
Person Address	Informatics and Analysis, Merck Research Lab, 770 Sumneytown Pike, West Point, PA, USA						
Person Roles	submitter						
Protocol Name	P-GSE31947-1	P-GSE31947-6	P-GSE31947-5	P-GSE31947-3	P-GSE31947-2	P-GSE31947-4	P-GSE31947-7
Protocol Description	ID_REF =  VALUE = normalized log10 ratio (Cy5/Cy3) representing test/reference	Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).	Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential	Total RNA extracted using Trizol following manufacturer's instructions	Aortas were isolated from the ApoE KO and control C57BL6 mice 16 weeks after feeding with HFD (HFD started at 8-week of age). The aorta of the ApoE KO mice showed atheroslerotic lesions whereas no lesion was observed with C57BL6 mice.	100 ng-input two-round RT/IVT RNA amplification protocol	Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	grow	labeling	feature_extraction
Experimental Factor Name	GENETIC BACKGROUND	GENOTYPE	AGE				
Experimental Factor Type	genetic background	genotype	age				
Publication Title	Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers.						
Publication Author List	Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, Meng Q, Peters M, He Y, Ni C, Slipetz D, Crackower MA, Houshyar H, Tan CM, Asante-Appiah E, O'Neill G, Luo MJ, Thieringer R, Yuan J, Chiu CS, Lum PY, Lamb J, Boie Y, Wilkinson HA, Schadt EE, Dai H, Roberts C						
PubMed ID	22806142						
Publication DOI	10.1038/msb.2012.24						
Comment[SecondaryAccession]	GSE31947						
Comment[GEOReleaseDate]	2013-03-22						
Comment[ArrayExpressSubmissionDate]	2011-09-07						
Comment[GEOLastUpdateDate]	2013-03-22						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE31947_ApoE_KO_6Samples.txt						
SDRF File	E-GEOD-31947.sdrf.txt