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Sample GSM792261 Query DataSets for GSM792261
Status Public on Sep 01, 2012
Title no lymph node metastasis patient 028, cancer, Homogenized
Sample type genomic
 
Source name surgically resected material
Organism Homo sapiens
Characteristics gender: female
source tissue: tongue
Stage: 2
metastasis: none
tissue: oral squamous cell carcinoma tumor from tongue
individual: patient 028
Treatment protocol Surgically resected tissue was frozen and stored in -80 C freezer. Frozen tissue was manually homogenized prior to extraction of genomic DNA.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from surgical materials using the QIAamp DNA Mini Kit (Qiagen) for tumor tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner 3000-7G.
Description Hybridized to 250K_Sty
Data processing Copy number analysis was performed using Genotyping Console software v4.0 (Affymetrix).
 
Submission date Sep 08, 2011
Last update date Sep 01, 2012
Contact name Ken Miyaguchi
E-mail(s) [email protected]
Phone 81-3-5803-4696
Organization name Tokyo Medical and Dental University
Lab Bioinformatics
Street address 5-45, Yushima 1, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8510
Country Japan
 
Platform ID GPL3720
Series (1)
GSE31984 Genome-wide copy number analysis for occult lymph node metastasis in oral squamous cell carcinoma

Data table header descriptions
ID_REF
VALUE Copy number status

Data table
ID_REF VALUE
SNP_A-1909444 1
SNP_A-2237149 1
SNP_A-4303947 1
SNP_A-2236359 1
SNP_A-2205441 1
SNP_A-2116190 2
SNP_A-4291020 2
SNP_A-2109914 2
SNP_A-2291997 2
SNP_A-4277872 2
SNP_A-2118217 2
SNP_A-1866065 2
SNP_A-2288244 2
SNP_A-1783407 2
SNP_A-2169457 2
SNP_A-4271011 2
SNP_A-2082515 2
SNP_A-1910751 2
SNP_A-2081399 2
SNP_A-2223642 2

Total number of rows: 238229

Table truncated, full table size 3722 Kbytes.




Supplementary file Size Download File type/resource
GSM792261_snp028t.CEL.gz 28.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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