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Sample GSM1414283 Query DataSets for GSM1414283
Status Public on Mar 01, 2015
Title 1832T
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.[G12G, G13R]
age at diagnosis: 40
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 2.07761
AFFX-SNP_10009702 2.0192
AFFX-SNP_10015773 1.87033
AFFX-SNP_10021569 1.46238
AFFX-SNP_10026879 1.88917
AFFX-SNP_10029725 1.45188
AFFX-SNP_10034687 1.48627
AFFX-SNP_10036267 2.29962
AFFX-SNP_10037362 2.58508
AFFX-SNP_10037636 2.55696
AFFX-SNP_10039349 1.5245
AFFX-SNP_10039442 1.64285
AFFX-SNP_10039933 1.9177
AFFX-SNP_10046830 2.2719
AFFX-SNP_10047363 1.22292
AFFX-SNP_10047841 2.51244
AFFX-SNP_10049334 1.28394
AFFX-SNP_10052664 2.07258
AFFX-SNP_10057887 2.0411
AFFX-SNP_10064911 1.60221

Total number of rows: 1855448

Table truncated, full table size 36359 Kbytes.

Supplementary file Size Download File type/resource
GSM1414283_1832T.CEL.gz 29.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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