Comment[ArrayExpressAccession]	E-GEOD-50647
MAGE-TAB Version	1.1					
Public Release Date	2013-10-28
Investigation Title	Transcriptome analysis of adipose tissues of A. actinomycetemcomitans- and C. pneumoniae-infected apoE-deficient mice					
Comment[Submitted Name]	Transcriptome analysis of adipose tissues of A. actinomycetemcomitans- and C. pneumoniae-infected apoE-deficient mice
Experiment Description	The 14-week experiment included three groups: 1) the Acute Cpn group, with one C. pneumoniae inoculation at the age of 9 wks; 2) the Chronic Cpn group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; and 3) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks. The mice were sacrificed at the age of 14 wks. The 24-week experiment included four groups: 1) the recurrent A. actinomycetemcomitans infection group, with ten  A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; 2) the chronic C. pneumoniae infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; 3) the combined chronic C. pneumoniae and recurrent A. actinomycetemcomitans infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks, and ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; and 4) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks, and ten 0.9% NaCl inoculations once a week from the age of 14 to 23 wks. The mice were sacrificed at the age of 24 wks.Epididymal and inguinal AT gene expression was analyzed using an Illumina Mouse WG-6 v2.0 platform. Total RNA obtained from inguinal and epididymal adipose tissues, samples from infected animals were compared to vehicle-inoculated 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	HyvM-CM-$rinen	HyvM-CM-$rinen	Pussinen			
Person First Name	Kati	Kati	Pirkko			
Person Mid Initials			J			
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	Institute of Dentistry, University of Helsinki					
Person Address	Institute of Dentistry, University of Helsinki, Biomedicum Helsinki 1, Haartmaninkatu 8, Helsinki, Finland					
Person Roles	submitter					
Protocol Name	P-GSE50647-1	P-GSE50647-4	P-GSE50647-5	P-GSE50647-2	P-GSE50647-3	P-GSE50647-6
Protocol Description	Quantile normalization. The software used to to perform quantile normalization were Anduril [1] and R [2]. 1: Kristian Ovaska, Marko Laakso et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Medicine 2010, 2:65. 2: R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/. ID_REF =  VALUE = quantile normalized signal	Standard Illumina labeling protocol. The cDNA was in vitro transcripted into cRNA using biotin-labeled nucleoside triphosphates.	Standard Illumina hybridization protocol. 5 M-5g of cRNA from each sample was hybridized at 58 M-0C overnight using the Illumina Whole-Genome Gene Expression Direct Hybridization Assay system with the six-sample BeadChip platform.	The mice were fed regular mouse chow ab libitum and maintained in a germ-free environment	Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). DNase treatment was performed on a column using the RNase-Free DNase Set (Qiagen) and again after RNA extraction using the DNA-freeM-bM-^DM-" Kit (Ambion). The RNA concentration was determined using a NanoDrop 1000 spectrophotometer (Thermo Scientific). The quality of total RNA was assessed by an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano Kit (Agilent Technologies).	Standard Illumina scannig protocol.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	AGE	ORGANISM PART	INFECTION			
Experimental Factor Type	age	organism part	infection			
Publication Title	The effect of proatherogenic pathogens on adipose tissue transcriptome and fatty acid distribution in apolipoprotein E-deficient mice.					
Publication Author List	HyvM-oM-?M-=rinen K, Tuomainen AM, Laitinen S, Alfthan G, Salminen I, Leinonen M, Saikku P, Kovanen PT, Jauhiainen M, Pussinen PJ					
PubMed ID	24131481					
Publication DOI	10.1186/1471-2164-14-709					
Comment[SecondaryAccession]	GSE50647					
Comment[GEOReleaseDate]	2013-10-28					
Comment[ArrayExpressSubmissionDate]	2013-09-06					
Comment[GEOLastUpdateDate]	2013-10-30					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE50647_non-normalized_data.txt					
SDRF File	E-GEOD-50647.sdrf.txt