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Sample GSM1414408 Query DataSets for GSM1414408
Status Public on Mar 01, 2015
Title IC229T
Sample type genomic
Source name Serous ovarian tumor
Organism Homo sapiens
Characteristics tissue: Tumor epithelium
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: WT
age at diagnosis: 64
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 1.9907
AFFX-SNP_10009702 1.80504
AFFX-SNP_10015773 2.5678
AFFX-SNP_10021569 2.23704
AFFX-SNP_10026879 1.92689
AFFX-SNP_10029725 1.55665
AFFX-SNP_10034687 2.33406
AFFX-SNP_10036267 1.91964
AFFX-SNP_10037362 2.58135
AFFX-SNP_10037636 1.81487
AFFX-SNP_10039349 1.80747
AFFX-SNP_10039442 2.43111
AFFX-SNP_10039933 1.88013
AFFX-SNP_10046830 1.96102
AFFX-SNP_10047363 2.21499
AFFX-SNP_10047841 2.11698
AFFX-SNP_10049334 2.09391
AFFX-SNP_10052664 1.84644
AFFX-SNP_10057887 2.24933
AFFX-SNP_10064911 2.54798

Total number of rows: 1855448

Table truncated, full table size 36344 Kbytes.

Supplementary file Size Download File type/resource
GSM1414408_IC229T.CEL.gz 30.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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