Comment[ArrayExpressAccession]	E-MTAB-2967					
MAGE-TAB Version	1.1					
Investigation Title	Genome wide pathway analysis using gene expression data of colonic mucosa in patients with Inflammatory Bowel Disease					
Comment[Submitted Name]	Genome wide pathway analysis using gene expression data of colonic mucosa in patients with Inflammatory Bowel Disease					
Experiment Description	To provide new steps on the role of altered gene expression in the pathogenesis of these diseases, we performed whole gene expression profiling by comparing the RNA from inflamed and non-inflamed colonic mucosa					
Experimental Design	disease state design					
Experimental Design Term Source REF	EFO					
Experimental Design Term Accession Number	EFO_0001756					
Comment[AEExperimentDisplayName]	Transcription profiling by array of RNA from inflamed and non-inflamed colonic mucosa					
Experimental Factor Name	disease	phenotype				
Experimental Factor Type	disease	phenotype				
Experimental Factor Term Source REF	EFO					
Experimental Factor Term Accession Number	EFO_0000408					
Person Last Name	Carella					
Person First Name	Massimo					
Person Mid Initials						
Person Email	m.carella@operapadrepio.it					
Person Phone	+39 0882 416350					
Person Fax	+39 0882 416350					
Person Address	Viale Cappuccini.1, San Giovanni Rotondo 71013, Foggia, Italy					
Person Affiliation						
Person Roles	submitter					
Date of Experiment	2010-05-31					
Public Release Date	2014-11-30					
PubMed ID	25901971					
Publication DOI	10.1097/MIB.0000000000000370					
Publication Author List	Palmieri O, Creanza TM, Bossa F, Palumbo O, Maglietta R, Ancona N, Corritore G, Latiano T, Martino G, Biscaglia G, Scimeca D, De Petris MP, Carella M, Annese V, Andriulli A, Latiano A					
Publication Title	Genome-wide Pathway Analysis Using Gene Expression Data of Colonic Mucosa in Patients with Inflammatory Bowel Disease					
Publication Status	published					
Publication Status Term Source REF	EFO					
Publication Status Term Accession Number	EFO_0001795					
Protocol Name	P-MTAB-41361	P-MTAB-41363	P-MTAB-41364	P-MTAB-41365	P-MTAB-41366	P-MTAB-41367
Protocol Type	growth protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	normalization data transformation protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Term Accession Number	EFO_0003789	EFO_0002944	EFO_0003813	EFO_0003816	EFO_0003815	EFO_0003814
Protocol Description	All tissue samples were snap-frozen in liquid nitrogen after resection and stored at -80C until use. 	Total RNA was extracted from each biopsy using Trizol (Invitrogen, Paisley, UK) or RNeasy Mini Kit (Qiagen), according to the manufacturers protocol.	GeneChip WT Terminal Labeling Kit	Gene expression data were normalized using Robust Multi-array Average (RMA) algorithm	Each end-labeled DNA fragment was hybridized the arrays	Each array was scanned to generate the raw data (.CEL file)
Protocol Hardware					GeneChip hybridization Oven 640	GeneChip Scanner 3000 7G
Protocol Software						GeneChip Command Console Software
Term Source Name	ArrayExpress	EFO				
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/				
Term Source Version						
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-MTAB-2967.sdrf.txt