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Sample GSM1414394 Query DataSets for GSM1414394
Status Public on Mar 01, 2015
Title 893T
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: 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 BIOTIN
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.
Description HYBRIDISED TO SNP6
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
E-mail(s) Sally.Hunter@petermac.org
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
ID_REF
VALUE SNP6 normalized copy number data

Data table
ID_REF VALUE
AFFX-SNP_10000979 1.63745
AFFX-SNP_10009702 1.79882
AFFX-SNP_10015773 1.36469
AFFX-SNP_10021569 2.73625
AFFX-SNP_10026879 1.69265
AFFX-SNP_10029725 1.44857
AFFX-SNP_10034687 1.66597
AFFX-SNP_10036267 1.82732
AFFX-SNP_10037362 1.97688
AFFX-SNP_10037636 2.05207
AFFX-SNP_10039349 1.89711
AFFX-SNP_10039442 1.94791
AFFX-SNP_10039933 1.7487
AFFX-SNP_10046830 2.47834
AFFX-SNP_10047363 2.11427
AFFX-SNP_10047841 2.77553
AFFX-SNP_10049334 1.64551
AFFX-SNP_10052664 2.26409
AFFX-SNP_10057887 1.60334
AFFX-SNP_10064911 1.98746

Total number of rows: 1855448

Table truncated, full table size 36341 Kbytes.




Supplementary file Size Download File type/resource
GSM1414394_893T.CEL.gz 29.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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