NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1414379 Query DataSets for GSM1414379
Status Public on Mar 01, 2015
Title 8632G
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: 61
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 1.81525
AFFX-SNP_10009702 2.01878
AFFX-SNP_10015773 1.57026
AFFX-SNP_10021569 2.57679
AFFX-SNP_10026879 1.84266
AFFX-SNP_10029725 1.96657
AFFX-SNP_10034687 2.24768
AFFX-SNP_10036267 1.61877
AFFX-SNP_10037362 1.6206
AFFX-SNP_10037636 2.25267
AFFX-SNP_10039349 2.50492
AFFX-SNP_10039442 1.5888
AFFX-SNP_10039933 2.11552
AFFX-SNP_10046830 1.87585
AFFX-SNP_10047363 2.00136
AFFX-SNP_10047841 1.83539
AFFX-SNP_10049334 2.02081
AFFX-SNP_10052664 2.09176
AFFX-SNP_10057887 1.92209
AFFX-SNP_10064911 2.05923

Total number of rows: 1855448

Table truncated, full table size 36320 Kbytes.




Supplementary file Size Download File type/resource
GSM1414379_8632G.CEL.gz 26.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap