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Sample GSM1414302 Query DataSets for GSM1414302
Status Public on Mar 01, 2015
Title 2602S
Sample type genomic
 
Source name Serous ovarian tumor
Organism Homo sapiens
Characteristics tissue: Tumor stroma
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: Wild-type
age at diagnosis: 68
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 2.25473
AFFX-SNP_10009702 1.87781
AFFX-SNP_10015773 1.35915
AFFX-SNP_10021569 2.32181
AFFX-SNP_10026879 2.22512
AFFX-SNP_10029725 1.34963
AFFX-SNP_10034687 2.45751
AFFX-SNP_10036267 2.41609
AFFX-SNP_10037362 2.04106
AFFX-SNP_10037636 2.55173
AFFX-SNP_10039349 1.58675
AFFX-SNP_10039442 1.76141
AFFX-SNP_10039933 2.2572
AFFX-SNP_10046830 2.4531
AFFX-SNP_10047363 1.13815
AFFX-SNP_10047841 1.87846
AFFX-SNP_10049334 2.13693
AFFX-SNP_10052664 1.76735
AFFX-SNP_10057887 2.25197
AFFX-SNP_10064911 1.58059

Total number of rows: 1855448

Table truncated, full table size 36323 Kbytes.




Supplementary file Size Download File type/resource
GSM1414302_2602S.CEL.gz 30.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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