Comment[ArrayExpressAccession]	E-GEOD-41408
MAGE-TAB Version	1.1							
Public Release Date	2013-02-11
Investigation Title	Co-expression of genes with ERG in prostate cancers							
Comment[Submitted Name]	Co-expression of genes with ERG in prostate cancers
Experiment Description	ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene. 48 Prostate cancer samples from radical prostatectomies were included in this study. These samples contained more than 70% cancer and less than 30% stromal tissue. Each sample was analyzed once.							
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	Jenster	Boormans	Trapman	Jenster				
Person First Name	Guido	Joost	Jan	Guido				
Person Mid Initials		L						
Person Email	g.jenster@erasmusmc.nl							
Person Affiliation	Erasmus MC							
Person Phone	31107043672							
Person Fax	31107044661							
Person Address	Urology, Erasmus MC, P.O. Box 2040, Rotterdam, Netherlands							
Person Roles	submitter							
Protocol Name	P-GSE41408-1	P-GSE41408-6	P-GSE41408-3	P-GSE41408-8	P-GSE41408-7	P-GSE41408-2	P-GSE41408-4	P-GSE41408-5
Protocol Description	ID_REF =  VALUE = RMA signal estimates from Partek Genome Suite	Standard hybridization protocol for Affymetrix human exon 1.0 ST	Samples are radical prostatectomy tissues directly taken from the patient	Cel files were processed using Partek RMA core probeset level probe group file: HuEx-1_0-st-v2.r2.pgf meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core	Standard scanner for Affymetrix human exon 1.0 ST	Samples were taken from the surgically removed prostate and fresh frozen in liq N2-cooled iso-pentane	The standard protocol from RNA-Bee (Campro Scientific) was used to extract total RNA	Standard whole transcript labeling protocol from Affymetrix human exon 1.0 ST
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	L	DEVELOPMENT OF METASTASIS	GLEASON SCORE	PSA PROGRESSION	PT-STAGE			
Experimental Factor Type	l	development of metastasis	gleason score	psa progression	pt-stage			
Publication Title	Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer.							
Publication Author List	Boormans JL, Korsten H, Ziel-van der Made AJ, van Leenders GJ, de Vos CV, Jenster G, Trapman J							
PubMed ID	23319146							
Publication DOI	10.1002/ijc.28025							
Comment[SecondaryAccession]	GSE41408							
Comment[GEOReleaseDate]	2013-02-11							
Comment[ArrayExpressSubmissionDate]	2012-10-09							
Comment[GEOLastUpdateDate]	2013-02-13							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-41408.sdrf.txt