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Sample GSM1414334 Query DataSets for GSM1414334
Status Public on Mar 01, 2015
Title 3905G
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: 46
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 1.88127
AFFX-SNP_10009702 2.42538
AFFX-SNP_10015773 1.98934
AFFX-SNP_10021569 1.41728
AFFX-SNP_10026879 2.14591
AFFX-SNP_10029725 2.2522
AFFX-SNP_10034687 2.29669
AFFX-SNP_10036267 1.5401
AFFX-SNP_10037362 2.46764
AFFX-SNP_10037636 2.00113
AFFX-SNP_10039349 2.65186
AFFX-SNP_10039442 2.44547
AFFX-SNP_10039933 2.39083
AFFX-SNP_10046830 2.17534
AFFX-SNP_10047363 2.7282
AFFX-SNP_10047841 2.35703
AFFX-SNP_10049334 2.08094
AFFX-SNP_10052664 1.88973
AFFX-SNP_10057887 2.1039
AFFX-SNP_10064911 2.0731

Total number of rows: 1855448

Table truncated, full table size 36320 Kbytes.




Supplementary file Size Download File type/resource
GSM1414334_3905G.CEL.gz 30.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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