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Sample GSM1414419 Query DataSets for GSM1414419
Status Public on Mar 01, 2015
Title IC558G
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: 55
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 1.61263
AFFX-SNP_10009702 2.11305
AFFX-SNP_10015773 1.87424
AFFX-SNP_10021569 2.10154
AFFX-SNP_10026879 1.61494
AFFX-SNP_10029725 1.56912
AFFX-SNP_10034687 2.86906
AFFX-SNP_10036267 1.73781
AFFX-SNP_10037362 2.22604
AFFX-SNP_10037636 2.40654
AFFX-SNP_10039349 1.86955
AFFX-SNP_10039442 1.93658
AFFX-SNP_10039933 1.86451
AFFX-SNP_10046830 1.50529
AFFX-SNP_10047363 1.84529
AFFX-SNP_10047841 2.04445
AFFX-SNP_10049334 2.64702
AFFX-SNP_10052664 2.3809
AFFX-SNP_10057887 1.68109
AFFX-SNP_10064911 1.66086

Total number of rows: 1855448

Table truncated, full table size 36330 Kbytes.

Supplementary file Size Download File type/resource
GSM1414419_IC558G.CEL.gz 26.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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