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Sample GSM1414411 Query DataSets for GSM1414411
Status Public on Mar 01, 2015
Title IC486G
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: 57
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 1.87993
AFFX-SNP_10009702 1.72031
AFFX-SNP_10015773 2.23117
AFFX-SNP_10021569 1.42782
AFFX-SNP_10026879 1.9154
AFFX-SNP_10029725 2.18286
AFFX-SNP_10034687 2.19853
AFFX-SNP_10036267 2.03811
AFFX-SNP_10037362 2.69029
AFFX-SNP_10037636 1.4282
AFFX-SNP_10039349 1.57126
AFFX-SNP_10039442 2.50994
AFFX-SNP_10039933 2.06596
AFFX-SNP_10046830 1.50505
AFFX-SNP_10047363 1.86584
AFFX-SNP_10047841 2.25412
AFFX-SNP_10049334 2.11368
AFFX-SNP_10052664 1.55621
AFFX-SNP_10057887 2.23654
AFFX-SNP_10064911 1.28972

Total number of rows: 1855448

Table truncated, full table size 36324 Kbytes.

Supplementary file Size Download File type/resource
GSM1414411_IC486G.CEL.gz 30.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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