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Sample GSM1414428 Query DataSets for GSM1414428
Status Public on Mar 01, 2015
Title IC515G
Sample type genomic
Source name Lymphocyte DNA
Organism Homo sapiens
Characteristics tissue: Peripheral Blood Lymphocytes
tumour histology: SEROUS
somatic ras/raf mutations: NA
age at diagnosis: 67
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 1.9373
AFFX-SNP_10009702 2.19386
AFFX-SNP_10015773 2.4777
AFFX-SNP_10021569 2.08168
AFFX-SNP_10026879 2.18968
AFFX-SNP_10029725 1.83872
AFFX-SNP_10034687 1.83572
AFFX-SNP_10036267 1.7812
AFFX-SNP_10037362 1.88349
AFFX-SNP_10037636 1.55873
AFFX-SNP_10039349 1.98536
AFFX-SNP_10039442 1.92102
AFFX-SNP_10039933 2.33048
AFFX-SNP_10046830 1.89558
AFFX-SNP_10047363 2.17407
AFFX-SNP_10047841 1.41603
AFFX-SNP_10049334 1.94955
AFFX-SNP_10052664 1.90804
AFFX-SNP_10057887 1.83644
AFFX-SNP_10064911 1.67085

Total number of rows: 1855448

Table truncated, full table size 36326 Kbytes.

Supplementary file Size Download File type/resource
GSM1414428_IC515G.CEL.gz 30.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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