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Sample GSM1414309 Query DataSets for GSM1414309
Status Public on Mar 01, 2015
Title 2713T
Sample type genomic
Source name Serous ovarian tumor
Organism Homo sapiens
Characteristics tissue: Tumor epithelium
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: KRAS p.G12D
age at diagnosis: 42
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 1.87533
AFFX-SNP_10009702 2.0293
AFFX-SNP_10015773 1.46562
AFFX-SNP_10021569 3.04848
AFFX-SNP_10026879 2.20552
AFFX-SNP_10029725 1.22635
AFFX-SNP_10034687 2.15743
AFFX-SNP_10036267 2.09628
AFFX-SNP_10037362 2.73339
AFFX-SNP_10037636 2.51263
AFFX-SNP_10039349 1.73826
AFFX-SNP_10039442 1.5357
AFFX-SNP_10039933 2.38276
AFFX-SNP_10046830 3.20694
AFFX-SNP_10047363 1.47199
AFFX-SNP_10047841 2.53451
AFFX-SNP_10049334 2.34041
AFFX-SNP_10052664 1.67192
AFFX-SNP_10057887 1.45809
AFFX-SNP_10064911 2.92154

Total number of rows: 1855448

Table truncated, full table size 36355 Kbytes.

Supplementary file Size Download File type/resource
GSM1414309_2713T.CEL.gz 29.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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