Comment[ArrayExpressAccession]	E-GEOD-49827
MAGE-TAB Version	1.1				
Public Release Date	2013-12-17
Investigation Title	Transformation of the Fallopian Tube Secretory Epithelium Leads to High-grade Serous Ovarian Cancer in BRCA/P53/PTEN Models				
Comment[Submitted Name]	Transformation of the Fallopian Tube Secretory Epithelium Leads to High-grade Serous Ovarian Cancer in BRCA/P53/PTEN Models
Experiment Description	Our study presents the first genetic models of de novo high-grade serous carcinomas (HGSC) that originate in fallopian tube secretory epithelial cells and recapitulate the key genetic alterations and precursor lesions characteristic of human invasive ovarian cancer.  Genomic copy number analysis, using array CGH, was performed on murine tumors in order to compare the overlap of copy number alterations between HGSC models and TCGA data. Array CGH was performed on genomic DNA isolated from murine HGSC tumors. Genomic DNA from three normal mouse fallopian tubes was pooled and used as the reference.				
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	Setlur	Setlur	Dinulescu	Drapkin	
Person First Name	Sunita	Sunita	Daniela	Ronny	
Person Mid Initials	R	R			
Person Email	ssetlur@partners.org				
Person Affiliation	Brigham and Women's Hospital				
Person Address	Brigham and Women's Hospital, 221 Longwood Avenue, Boston, USA				
Person Roles	submitter				
Protocol Name	P-GSE49827-1	P-GSE49827-3	P-GSE49827-4	P-GSE49827-2	P-GSE49827-5
Protocol Description	Probes signal intensities were obtained using the feature extraction software from Agilent for further analysis. In Feature Extraction software, for CGH data, linear normalization method is used.  Analysis was performed with Nexus software (BioDiscovery), for identification of copy number alterations. FASST2 segmentation algorithm was applied by setting the following parameters. A minimum number of 5 probes per segment were used to call a copy number aberration with significance threshold of 5x10-6. We used log ratio cut offs of M-BM-10.3 to call one copy gain/loss and M-BM-10.7 to call high gain/ homozygous loss. ID_REF =  VALUE = normalized log2 ratio (Cy5/Cy3) representing test/reference	Briefly, reference and test DNA were first fragmented using a heat block at 95M-0C for 5 minutes and then labeled using Cyanine3 / Cyanine5 fluorescence labeled nucleotides respectively, according to the BioPrime Array CGH Genomic Labeling protocol (Invitrogen).Labeled DNA was purified using AmiconM-. Ultra-0.5 30k purification columns (Millipore).	Test and reference DNA were combined and hybridized to the Agilent 1M mouse catalog array for 40 hours at 65M-0C. The array slides were then washed and scanned.	Mouse genomic DNA was isolated using Gentra Puregene Cell Kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions	Arrays were scanned using the Agilent G2565AA scanner
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENOTYPE				
Experimental Factor Type	genotype				
Comment[SecondaryAccession]	GSE49827				
Comment[GEOReleaseDate]	2013-12-17				
Comment[ArrayExpressSubmissionDate]	2013-08-13				
Comment[GEOLastUpdateDate]	2013-12-17				
Comment[AEExperimentType]	comparative genomic hybridization by array				
SDRF File	E-GEOD-49827.sdrf.txt