Investigation Title	Transcription profiling of mouse tissues - GNF Mouse GeneAtlas V3					
Comment[Submitted Name]	GNF Mouse GeneAtlas V3					
Experimental Design	organism_part_comparison_design	transcription profiling by array				
Experimental Design Term Source REF		EFO				
Comment[AEExperimentType]	transcription profiling by array					
Comment[AEExperimentDisplayName]	Transcription profiling by array of Mus musculus tissues - GNF Mouse GeneAtlas V3					
Comment[ArrayExpressReleaseDate]	2008-06-11					
Comment[SecondaryAccession]	GSE10246					
Comment[AEMIAMESCORE]	4					
Comment[ArrayExpressAccession]	E-GEOD-10246					
Comment[MAGETAB TimeStamp_Version]	2010-07-30 00:00:55 Last Changed Rev: 13058					
Experimental Factor Name	organism part	cell type	cell line	disease state	compound	time
Experimental Factor Type	organism part	cell type	cell line	disease state	compound	time
Experimental Factor Term Source REF						
Person Last Name	Walker					
Person First Name	John					
Person Mid Initials	R.					
Person Email	jwalker@gnf.org					
Person Phone						
Person Fax						
Person Address	"RNA Profiling Group, ,Genomics Institute of the Novartis Research Foundation,10675 John Jay Hopkins,San Diego,92121,USA"					
Person Affiliation	Genomics Institute of the Novartis Research Foundation					
Person Roles	submitter					
Person Roles Term Source REF	The MGED Ontology					
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	2008-06-11					
PubMed ID	18442421					
Publication DOI						
Publication Author List	"Lattin JE, Schroder K, Su AI, Walker JR, Zhang J, Wiltshire T, Saijo K, Glass CK, Hume DA, Kellie S, Sweet MJ."					
Publication Title	Expression analysis of G Protein-Coupled Receptors in mouse macrophages.					
Publication Status						
Publication Status Term Source REF						
Experiment Description	"Monocytes and macrophages express an extensive repertoire of G Protein-Coupled Receptors (GPCRs) that regulate inflammation and immunity. In this study we performed a systematic microarray analysis of GPCR expression in primary mouse tissues to identify family members that are either enriched in macrophages compared to a panel of other cell types, or are regulated by an inflammatory stimulus, the bacterial product lipopolysaccharide (LPS). Experiment Overall Design: Multiple tissues were taken from naïve male C57BL6 mice for hybridization to MOE430_2 arrays"					
Protocol Name	P-G10246-1	P-G10246-3	P-G10246-2	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6	
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	"All cell lines and tissues were sourced from 8-10 week old male C57Bl/6 mice, with the exception of female-specific organs, which were sourced from female mice. All procedures were carried out in accordance with local guidelines for animal research. For female tissues, material was pooled from three females, and for each female, on average four embryos resulting in four umbilical cords and placentas were obtained. For other tissues, material was derived from a pool of three males. Biological replicates were defined as independent RNA preparations from independent pools of mice. Technical replicates were defined as independent amplifications from the sample RNA sample."	"RNA extraction from mammalian cells or tissues was performed using RNeasy kits (Qiagen, Valencia, CA) or a standard Trizol protocol. If tissue amounts were more than 50 mg per mouse when dissected, tissues were pulverized while frozen. RNA was prepared separately for every mouse in order to identify samples with potentially degraded RNA. Trizol-extracted RNA was purified with a Qiagen RNeasy column. For bone marrow macrophages, osteoblasts, and osteoclasts, contaminating genomic DNA was removed during the RNeasy cleanup using DNaseI (Qiagen, Valencia, CA). The integrity and concentration of RNA was determined via microfluidic analysis on a bio-analyser (Agilent Technologies, Palo Alto, CA) or by analysis on a BioRad Experion. Pooling occurred at the RNA level."	"For samples containing more than two Âμg total RNA available after pooling, standard Affymetrix single amplification was performed using two Âμg total RNA. For pooled samples containing less than two Âμg total RNA, 100 ng total RNA (or 50 ng for thymocyte_SP_CD8+) was used in a standard Affymetrix double amplification protocol."	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters						
Protocol Hardware						
Protocol Software				MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact						
Protocol Term Source REF				mo		
SDRF File	E-GEOD-10246.sdrf.txt					
Term Source Name	The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	mo	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version