Comment[ArrayExpressAccession] E-MTAB-1584 MAGE-TAB Version 1.1 Investigation Title BIN-67 small cell ovarian carcinoma SNP array Comment[Submitted Name] BIN-67 small cell ovarian carcinoma SNP array 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. Chromosomal anomalies in BIN-67 cells were inferred using the Infinium? genotyping technology with the HumanHap300-Duo Genotyping BeadChip (Illumina, San Diego, CA, USA). This BeadChip contains about 318,000 genetic markers within approximately a 5 kb median SNP spacing. Genotyping and imaging using BeadStudio Data Analysis software (Illumina, San Diego, CA, USA) were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC). Experimental Design disease_state_design in_vitro_design genotyping_design Comment[AEExperimentType] genotyping by array Comment[AEExperimentDisplayName] Genotyping by array of human BIN-67 small cell ovarian carcinoma to investigate genomic stability Experimental Factor Name Experimental Factor Type Quality Control Type Quality Control Term Source REF EFO Public Release Date 2013-09-24 Person Last Name Arcand Tonin Person First Name Suzanna Patricia Person Mid Initials L N Person Email suzanna.arcand@mail.mcgill.ca patricia.tonin@mcgill.ca Person Phone 1-514-934-1934 ext.44201 1-514-934-1934 x44069 Person Address Medical Genetics, Montreal General Hospital, Room L10-132, 1650 Cedar Avenue, Montreal, Quebec H3G 1A4, Canada Medical Genetics, Montreal General Hospital, Room L10-132, 1650 Cedar Avenue, Montreal, Quebec H3G 1A4, Canada Person Affiliation RI-MUHC Departments of Medicine and Human Genetics, McGill University, Montreal, Canada Person Roles submitter primary contact PubMed ID 23433318 Publication Author List Gamwell LF, Gambaro K, Merziotis M, Crane C, Arcand SL, Bourada V, Davis C, Squire JA, Huntsman DG, Tonin PN, Vanderhyden BC. Publication Title Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Publication Status in press Protocol Name P-MTAB-32063 P-MTAB-32064 P-MTAB-32065 Protocol Type growth nucleic acid extraction protocol normalization data transformation protocol Protocol Description 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). DNA was extracted using the Gentra Puregene kit (QIAGEN). Purified DNA was dissolved and eluted in DNA hydration solution and stored at 4?C. Image data was analyzed using Beadstudio 2.2.22 (Illumina). This samples log_R_ratio values and B-allele frequencies were generated against the Illumina reference panel. Genotyping analysis was performed using the Genome Viewer module in BeadStudio Data Analysis software v2.2.22 (Illumina, San Diego, CA, USA.). The software aligns genotyping data for each marker with genomic map coordinates based on March 2006 NCBI36/hg18 (Build 36.1) assembly of the human reference sequence (genome.ucsc.edu/cgi-bin/hgGateway). An image file was created for inferring genomic rearrangements based on the allele frequency and copy number (Log R ratios) for each marker assayed. LOH was inferred by B allele frequency, where values that deviate from 0.5 (less than 0.4 and greater than 0.6) indicate allelic imbalance when reviewed for a series of adjacently mapped markers. Breakpoints were inferred based on deviation of allele frequencies relative to those of adjacently mapped markers. Log R ratios deviating from 0 suggest copy gain or loss. Protocol Term Source REF EFO EFO EFO Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/EFO SDRF File E-MTAB-1584.sdrf.txt