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Sample GSM1414329 Query DataSets for GSM1414329
Status Public on Mar 01, 2015
Title 2989G
Sample type genomic
Source name Lymphocyte DNA
Organism Homo sapiens
Characteristics tissue: Peripheral Blood Lymphocytes
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: NA
age at diagnosis: 47
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 2.06133
AFFX-SNP_10009702 1.86494
AFFX-SNP_10015773 1.84771
AFFX-SNP_10021569 2.17352
AFFX-SNP_10026879 1.9995
AFFX-SNP_10029725 1.57087
AFFX-SNP_10034687 1.86948
AFFX-SNP_10036267 1.81049
AFFX-SNP_10037362 1.99963
AFFX-SNP_10037636 2.02107
AFFX-SNP_10039349 1.58826
AFFX-SNP_10039442 1.99113
AFFX-SNP_10039933 1.76617
AFFX-SNP_10046830 2.77274
AFFX-SNP_10047363 1.74818
AFFX-SNP_10047841 2.13431
AFFX-SNP_10049334 2.16143
AFFX-SNP_10052664 1.76782
AFFX-SNP_10057887 2.13745
AFFX-SNP_10064911 2.59449

Total number of rows: 1855448

Table truncated, full table size 36321 Kbytes.

Supplementary file Size Download File type/resource
GSM1414329_2989G.CEL.gz 30.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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