Comment[ArrayExpressAccession]	E-GEOD-47633
MAGE-TAB Version	1.1																				
Public Release Date	2013-06-05
Investigation Title	The genomic and transcriptomic dynamics of treatment-naïve epithelial ovarian cancer																				
Comment[Submitted Name]	The genomic and transcriptomic dynamics of treatment-naïve epithelial ovarian cancer
Experiment Description	We reveal three-dimensional patterns of tumour growth by exploiting the unique metastasizing patterns of treatment naïve stage IIIC/IV epithelial ovarian cancer. We performed topographic mapping of structural genomic rearrangements, coding mutations, copy number changes and RNA expression in biopsies derived from 27 primary and metastatic sites across three patients. Based on somatic genomic changes, we performed sample clustering and obtained unique insight in natural tumour growth and spread. Based on extensive multi-level profiling, our data highlight the diverse modes of epithelial ovarian cancer development before applying selective pressure from therapy. We performed SNP array analysis on tumor biopsies from 3 patients (P1, P2, P3) with advanced stage ovarian cancer. This submission includes SNP data for 26 tumor biopsies and 5 normal tissue samples.																				
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	Kloosterman	Hoogstraat	de Pagter	Cirkel	van Roosmalen	Harkins	Duran	Kreeftmeijer	Renkens	Witteveen	Lee	Nijman	Guy	van 't Slot	Jonges	Lolkema	Koudijs	Zweemer	Voest	Cuppen	Kloosterman
Person First Name	Wigard	Marlous	Mirjam	Geert	Markus	Tim	Karen	Jennifer	Ivo	Els	Clarence	Isaac	Tanisha	Ruben	Trudy	Martijn	Marco	Ronald	Emile	Edwin	Wigard
Person Mid Initials					J					P		J									P
Person Email	w.kloosterman@umcutrecht.nl																				
Person Affiliation	University Medical Center Utrecht																				
Person Address	University Medical Center Utrecht, Universiteitsweg 100, Utrecht, Netherlands																				
Person Roles	submitter																				
Protocol Name	P-GSE47633-1	P-GSE47633-3	P-GSE47633-4	P-GSE47633-2	P-GSE47633-5																
Protocol Description	Data processing was done using GenomeStudio (Illumina). ID_REF =  VALUE = Genotype: AA, AB, BB, or NC (no call) Score =  Theta =  R =  B Allele Freq =  Log R Ratio = 	200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation, the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).	RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).	Extraction of genomic DNA from fresh frozen tissue was performed using QIAGEN Genomic DNA kit.	After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iScan (Illumina).																
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol																
Experimental Factor Name	PATIENT IDENTIFIER	TUMOR STAGE	ORGANISM PART																		
Experimental Factor Type	patient identifier	tumor stage	organism part																		
Comment[SecondaryAccession]	GSE47633																				
Comment[GEOReleaseDate]	2013-06-05																				
Comment[ArrayExpressSubmissionDate]	2013-06-04																				
Comment[GEOLastUpdateDate]	2013-06-05																				
Comment[AEExperimentType]	genotyping by array																				
Comment[AdditionalFile:Data1]	GSE47633_raw_signals.txt																				
SDRF File	E-GEOD-47633.sdrf.txt