Comment[ArrayExpressAccession]	E-MEXP-3872
Investigation Title	BIN-67 small cell ovarian carcinoma Expression array
Comment[Submitted Name]	BIN-67 small cell ovarian carcinoma Expression array
Comment[AEExperimentDisplayName]	Transcription profiling by array of human BIN-67 small cell ovarian carcinoma to investigate gene expression
Comment[MIAMExpressLogin]	sarcand
Comment[MIAMExpressSubmissionID]	8705
Experiment Description	The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Microarray expression analysis was performed using the GeneChip? Human Genome U133 Plus 2.0 Array (Affymetrix?, Santa Clara, CA) with total RNA from BIN-67 cells. Hybridization and scanning were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC). Gene expression levels were determined from the scanned images using Affymetrix? Microarray Suite (MAS) version 5.0 software expression algorithm (Affymetrix?, Santa Clara, CA). Gene expression profiles were compared with Affymetrix U133 Plus 2.0 (MAS5.0) generated expression profiles (similarly normalized) from 10 human normal ovarian surface epithelial (OSE) cell brushings available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress/), accession number E-GEOD-18520.
Experimental Design	disease_state_design	array_platform_variation_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array
Experimental Factor Name
Experimental Factor Type
Person Last Name	Arcand
Person First Name	Suzanna
Person Email	suzanna.arcand@mail.mcgill.ca
Person Phone	514-934-1934 X44201
Person Affiliation	RI-MUHC
Person Address	Research, 1650 Cedar ave. Room L3-401, Montreal, Montreal, H3G1A4, Canada
Person Roles	submitter
Person Roles Term Source REF	MGED Ontology
Quality Control Type
Public Release Date	2013-09-24
Comment[ArrayExpressSubmissionDate]	2013-03-26 05:40:32
Publication Title	Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics.
Publication Status	in press
Protocol Name	P-MTAB-31887	P-MTAB-31888	P-MTAB-31889
Protocol Description	Total RNA was isolated with TRIzol (Invitrogen) and purified with RNeasy MinElute Cleanup kit (Qiagen). RNA quality was verified on BioAnalyzer Nano chip (Agilent Technologies).<br>(Parameters: Extracted product = total RNA, Amplification = none)	BIN-67 cell line was cultured from frozen stock in DMEM supplemented with 20% fetal calf serum and enriched with 20% Ham?s F12 medium (Sigma Chemical Co.,St Louis, MO).<br>(Parameters: time unit = seconds, min temperature = 37, temperature unit = C, media = DMEM, Ham's F12)	The data were normalized and the absolute call (P, M, or A) generated with Affymetrix Microarray Suite version 5.0 (MAS 5.0) .
Protocol Type	nucleic_acid_extraction	grow	bioassay_data_transformation
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology
Term Source Name	MGED Ontology	ArrayExpress
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress
SDRF File	E-MEXP-3872.sdrf.txt