Comment[ArrayExpressAccession]	E-GEOD-44076
MAGE-TAB Version	1.1											
Public Release Date	2014-03-14
Investigation Title	Gene expression data from healthy, adjacent normal and tumor colon cells											
Comment[Submitted Name]	Gene expression data from healthy, adjacent normal and tumor colon cells
Experiment Description	Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae, were obtained through Affymetrix Human Genome U219 Arrays. This dataset is in the context of the COLONOMICS project and to query additional information you can visit the project website www.colonomics.org. Colon tumor and adjacent paired normal mucosa tissues samples used in this study were selected from a series of cases with a new diagnosis of colorectal adenocarcinoma histologically confirmed. Included cases were from a homogenous series of patients with more than three years of follow up, early stage (II), without neoadjuvant chemotherapy and microsatellite stable colon cancer. Additionally, samples of colon mucosa from 50 healthy donors without colonic lesions were obtained during colonoscopy.											
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	Romera	SolM-CM-)	Crous-Bou	Sanz-Pamplona	ParM-CM-)	Cordero	GuinM-CM-3	Berenguer	Closa	Olivares	Lopez-Doriga	Moreno
Person First Name	David	Xavi	Marta	Rebeca	Laia	David	Elisabet	Antoni	AdriM-CM- 	David	Adriana	Victor
Person Mid Initials	Cordero											
Person Email	dcordero@iconcologia.net											
Person Affiliation	Catalan Institute Of Oncology											
Person Phone	34932607186											
Person Address	Biomarkers and Susceptibilty Unit, Catalan Institute Of Oncology, Av. Gran Via 199-203, Barcelona, Catalonia, Spain											
Person Roles	submitter											
Protocol Name	P-GSE44076-1	P-GSE44076-3	P-GSE44076-4	P-GSE44076-2	P-GSE44076-5							
Protocol Description	The Robust Multi-array Average (RMA) algorithm was used for data normalization through R and Bioconductor. ID_REF =  VALUE = log2 RMA signal	RNA was labeled with the 3'-IVT Labeling Kit (Affymetrix, Santa Clara, USA) following the manufacturer's protocols.	RNA hybridization was performed through the Affymetrix Human Genome U219 microarrays, using the 96-array plate format on the GeneTitan system and following the manufacturer's recommendations (Affymetrix, Santa Clara, USA). A blocked experimental design was implemented to avoid biases.	RNA was extracted from tissue samples using a miRCURYM-bM-^DM-" RNA Isolation Kit (Exiqon) according to manufacturerM-bM-^@M-^Ys protocol, quantified by NanoDropM-. ND-1000 Spectrophotometer (Nanodrop technologies, Wilmington, DE) and stored at -80M-0C. The quality of these RNA samples was further checked using RNA 600 Nano chip (Agilent Bioanalyzer) and was confirmed by gel electrophoresis.	Human Genome U219 array plates were scanned according to manufacturer's recommendations (Affymetrix, Santa Clara, USA).							
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol							
Experimental Factor Name	INDIVIDUAL ID	SAMPLE TYPE	LOCATION	STAGE	AGE	SEX						
Experimental Factor Type	individual id	sample type	location	Stage	age	sex						
Publication Title	Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer.											
Publication Author List	Sanz-Pamplona R, Berenguer A, Cordero D, MollevM-oM-?M-= DG, Crous-Bou M, Sole X, ParM-oM-?M-=-Brunet L, Guino E, Salazar R, Santos C, de Oca J, Sanjuan X, Rodriguez-Moranta F, Moreno V											
PubMed ID	24597571											
Publication DOI	10.1186/1476-4598-13-46											
Comment[SecondaryAccession]	GSE44076											
Comment[GEOReleaseDate]	2014-03-14											
Comment[ArrayExpressSubmissionDate]	2013-02-05											
Comment[GEOLastUpdateDate]	2014-03-15											
Comment[AEExperimentType]	transcription profiling by array											
SDRF File	E-GEOD-44076.sdrf.txt