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Sample GSM1414294 Query DataSets for GSM1414294
Status Public on Mar 01, 2015
Title 2244G
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: 44
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 BIOTIN
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.
Description HYBRIDISED TO SNP6
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
E-mail(s) Sally.Hunter@petermac.org
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
ID_REF
VALUE SNP6 normalized copy number data

Data table
ID_REF VALUE
AFFX-SNP_10000979 2.09247
AFFX-SNP_10009702 2.00421
AFFX-SNP_10015773 2.02038
AFFX-SNP_10021569 2.56012
AFFX-SNP_10026879 2.13762
AFFX-SNP_10029725 2.04214
AFFX-SNP_10034687 2.37811
AFFX-SNP_10036267 1.72496
AFFX-SNP_10037362 2.17772
AFFX-SNP_10037636 2.35214
AFFX-SNP_10039349 2.0499
AFFX-SNP_10039442 1.72457
AFFX-SNP_10039933 1.67778
AFFX-SNP_10046830 2.11956
AFFX-SNP_10047363 2.3446
AFFX-SNP_10047841 1.5837
AFFX-SNP_10049334 1.67014
AFFX-SNP_10052664 2.28655
AFFX-SNP_10057887 1.90442
AFFX-SNP_10064911 1.84818

Total number of rows: 1855448

Table truncated, full table size 36322 Kbytes.




Supplementary file Size Download File type/resource
GSM1414294_2244G.CEL.gz 25.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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