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Sample GSM1414339 Query DataSets for GSM1414339
Status Public on Mar 01, 2015
Title 3964T
Sample type genomic
Source name Serous ovarian tumor
Organism Homo sapiens
Characteristics tissue: Tumor epithelium
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: BRAF p.V600E
age at diagnosis: 22
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumours stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.
Label protocol As per manufacturer's recommendations (Affymetrix)
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.
Submission date Jun 17, 2014
Last update date Mar 01, 2015
Contact name Sally Hunter
Organization name Peter MacCallum Cancer Centre
Department Research
Lab Cancer Genetics
Street address 7 St Andrew's Pl
City Melbourne
State/province VIC
ZIP/Postal code 3002
Country Australia
Platform ID GPL6801
Series (1)
GSE58579 High-resolution genome-wide copy number analysis of low grade serous ovarian tumours

Data table header descriptions
VALUE SNP6 normalized copy number data

Data table
AFFX-SNP_10000979 2.72528
AFFX-SNP_10009702 1.75147
AFFX-SNP_10015773 2.32765
AFFX-SNP_10021569 2.13668
AFFX-SNP_10026879 2.44804
AFFX-SNP_10029725 1.84984
AFFX-SNP_10034687 3.3415
AFFX-SNP_10036267 2.71331
AFFX-SNP_10037362 2.55085
AFFX-SNP_10037636 1.47447
AFFX-SNP_10039349 1.78803
AFFX-SNP_10039442 2.89952
AFFX-SNP_10039933 2.02179
AFFX-SNP_10046830 2.83635
AFFX-SNP_10047363 2.36075
AFFX-SNP_10047841 2.11516
AFFX-SNP_10049334 2.19319
AFFX-SNP_10052664 2.40225
AFFX-SNP_10057887 2.03468
AFFX-SNP_10064911 1.73714

Total number of rows: 1855448

Table truncated, full table size 36323 Kbytes.

Supplementary file Size Download File type/resource
GSM1414339_3964T.CEL.gz 29.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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