Investigation Title	"Transcription profiling by array of human normal pre-frontal cortex, liver, and colon tissues and colon tumors"					
Comment[Submitted Name]	"Expression data from human normal pre-frontal cortex, liver, and colon tissues and colon tumors"					
Experimental Design	co-expression_design	transcription profiling by array				
Experimental Design Term Source REF	The MGED Ontology	EFO				
Comment[AEExperimentType]	transcription profiling by array					
Comment[AEMIAMESCORE]	4					
Comment[SecondaryAccession]						
Comment[SecondaryAccession]	GSE13471					
Comment[ArrayExpressReleaseDate]	2009-01-23					
Comment[ArrayExpressAccession]	E-GEOD-13471					
Comment[MAGETAB TimeStamp_Version]	2010-11-29 01:24:08 Last Changed Rev: 14857					
Experimental Factor Name	organism part					
Experimental Factor Type	organism part					
Experimental Factor Term Source REF						
Person Last Name	irizarry					
Person First Name	rafael					
Person Mid Initials						
Person Email	rafa@jhu.edu					
Person Phone						
Person Fax						
Person Address	"Johns Hopkins University,  , Baltimore, 21209, USA"					
Person Affiliation						
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	2009-01-23					
PubMed ID	19151715					
Publication DOI						
Publication Author List	"Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP."					
Publication Title	The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.					
Publication Status						
Publication Status Term Source REF						
Experiment Description	"DNA methylation, at CpG islands and promoters, is often inversely correlated with gene expression. We used expression microarrays to determine the relationship between DNA methylation and gene expression in 5 normal prefrontal cortex samples and 5 normal liver samples from the same individuals as well as between 4 colon tumor and matched normal colon mucosa (from the same individuals). Experiment Overall Design: We isolated RNA from pre-frontal cortex and liver tissue from 5 individuals for which we have genome-wide DNA methylation data and hybridized to Affymetrix gene expression microarrays. Similarly, we isolated RNA from 4 tumor and matched normal colon samples that we have genome-wide DNA methylation data..<br><br>This experiment was reloaded in November 2010 after additional curation."					
Protocol Name	P-G13471-2	P-G13471-1	P-G13471-4	P-G13471-3	P-AFFY-6	
Protocol Type	specified_biomaterial_action	grow	nucleic_acid_extraction	labeling	feature_extraction	
Protocol Description	no treatment	no growth	Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications	"Preparation of biotinylated cRNA was performed according to the standard (one-cycle) Affymetrix U133A 2.0 sample preparation protocol, starting with 1ug of total RNA"		
Protocol Parameters						
Protocol Hardware						
Protocol Software					MicroArraySuite 5.0	
Protocol Contact						
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology		
SDRF File	E-GEOD-13471.sdrf.txt					
Term Source Name		The MGED Ontology	EFO	ArrayExpress	The MGED Ontology	EFO
Term Source File		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/
Term Source Version