Investigation Title	Transcription profiling by array of mouse cell types and tissues (GNF/Novartis)										
Comment[Submitted Name]	Walker: Analysis of Murine Transcriptome										
Experimental Design	organism_part_comparison_design	transcription profiling									
Experimental Design Term Source REF	mo										
Comment[AEExperimentType]	transcription profiling by array										
Comment[ArrayExpressReleaseDate]											
Comment[AEMIAMESCORE]	5										
Comment[ArrayExpressAccession]	E-AFMX-4										
Comment[MAGETAB TimeStamp_Version]	2009-09-14 13:39:21 Last Changed Rev: 6528										
Experimental Factor Name	OrganismPart	DevelopmentalStage									
Experimental Factor Type	organism part	developmental stage									
Experimental Factor Term Source REF											
Person Last Name	Walker										
Person First Name	John										
Person Mid Initials											
Person Email	miamexpress@ebi.ac.uk										
Person Phone											
Person Fax											
Person Address											
Person Affiliation	Genomics Institute of the Novartis Research Foundation										
Person Roles	submitter										
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	2005-02-16										
PubMed ID	15075390										
Publication DOI	15075390										
Publication Author List	"Andrew I. Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A. Ching, David Block, Jie Zhang, Richard Soden, Mimi Hayakawa, Gabriel Kreiman, Michael P. Cooke, John R. Walker, and John B. Hogenesch "										
Publication Title	A gene atlas of the mouse and human protein-encoding transcriptomes										
Publication Status	journal_article										
Publication Status Term Source REF	mo										
Experiment Description	"The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting."										
Protocol Name	P-AFMX-4	P-AFFY-2	Affymetrix:Protocol:Hybridization-Unknown	Affymetrix:Protocol:Percentile	Affymetrix:Protocol:ExpressionStat						
Protocol Type	nucleic_acid_extraction	labeling	hybridization	feature_extraction	bioassay_data_transformation						
Protocol Description	"Adult (10-12 week) mouse tissue samples were independently generated from 2 groups of 4 male and 3 female C57/BL6 mice by dissection and tissues subsequently quick frozen on dry ice. Tissues were pulverized while frozen, and Total RNA were extracted with  Trizol (Invitrogen, Carlsbad, CA) using approximately 100 mg tissue, then further processed using RNeasy according to manufacturer's protocol (QIAGEN)."										
Protocol Parameters				Lower left corner x coordinate;Lower left corner y coordinate;Algorithm name;Percentile;Upper right corner y coordinate;Upper right corner x coordinate;Lower right corner x coordinate;Cell margin;Upper left corner y coordinate;Lower right corner y coordinate;Outlier high;Upper left corner x coordinate;Outlier low;	Algorithm name;Alpha2;Gamma1L;Scale factor;Alpha1;Gamma2H;Gamma2L;Baseline file;Mask file;Perturbation;Tau;Algorithm version;Gamma1H;Normalization factor;						
Protocol Hardware											
Protocol Software			MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0						
Protocol Contact											
Protocol Term Source REF			mo		The MGED Ontology						
SDRF File	E-AFMX-4.sdrf.txt										
Term Source Name	NCI_thesaurus	mo	nci_thesaurus		ma	efo.obo	NCI Thesaurus	cbil_cv	ArrayExpress	The MGED Ontology	EFO
Term Source File	ncithesaurus.obo.alt	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do		http://berkeleybop.org/cgi-bin/obofoundry/detail.cgi?id=adult_mouse_anatomy	/nfs/ma/ma-exp/GEOImportDownload/efo.obo	http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do	http://www.cbil.upenn.edu/anatomy.php3	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/efo.owl
Term Source Version