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Sample GSM1414362 Query DataSets for GSM1414362
Status Public on Mar 01, 2015
Title 5594S
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: 73
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 1.77553
AFFX-SNP_10009702 2.30579
AFFX-SNP_10015773 1.85086
AFFX-SNP_10021569 1.5931
AFFX-SNP_10026879 1.61534
AFFX-SNP_10029725 1.85641
AFFX-SNP_10034687 1.6891
AFFX-SNP_10036267 1.79905
AFFX-SNP_10037362 2.09063
AFFX-SNP_10037636 2.99072
AFFX-SNP_10039349 1.96294
AFFX-SNP_10039442 2.25332
AFFX-SNP_10039933 1.72165
AFFX-SNP_10046830 2.17178
AFFX-SNP_10047363 1.85924
AFFX-SNP_10047841 1.28581
AFFX-SNP_10049334 1.85738
AFFX-SNP_10052664 2.39059
AFFX-SNP_10057887 2.11216
AFFX-SNP_10064911 1.7802

Total number of rows: 1855448

Table truncated, full table size 36335 Kbytes.




Supplementary file Size Download File type/resource
GSM1414362_5594S.CEL.gz 24.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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