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Sample GSM617682 Query DataSets for GSM617682
Status Public on Sep 01, 2011
Title OSCC tumor_OR1286
Sample type genomic
Source name OSCC specimens
Organism Homo sapiens
Characteristics disease state: tumor
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (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 Hybridized to Affymetrix SNP6.0
Data processing We used Partek to detect copy number variation. We used birdseed algorithm for calling SNP 6.0, which is suggested standard algorithm, and birdseed is embedded in software of Genotyping Console (GTC) or Affymetrix Power Tool (APT) which all provide by affymetrix company. The reported summarized intensity are separated into A intensity and B intensity, and results in calling into AA, AB, or BB categories.
Submission date Nov 04, 2010
Last update date Sep 01, 2011
Contact name Chien-Hua Peng
Organization name Chang Gung Memorial Hospital
Street address No. 5, Fu-Hsing ST.
City Taoyuan
ZIP/Postal code 33305
Country Taiwan
Platform ID GPL6801
Series (2)
GSE25103 Affymetrix SNP array data for oral squamous cell carcinoma
GSE25104 Expression and SNP array data for oral squamous cell carcinoma

Data table header descriptions
VALUE genotype call

Data table
ID_REF VALUE signalA signalB
AFFX-SNP_10000979 AA 1007.04791 201.17387
AFFX-SNP_10009702 AA 1360.02953 332.12094
AFFX-SNP_10015773 AB 1555.36692 1701.44943
AFFX-SNP_10021569 AA 737.88551 397.69472
AFFX-SNP_10026879 BB 640.65922 2004.88864
AFFX-SNP_10029725 AA 841.59166 315.75212
AFFX-SNP_10034687 AB 549.51354 658.15559
AFFX-SNP_10036267 BB 355.20649 801.08933
AFFX-SNP_10037362 BB 984.74956 3716.39583
AFFX-SNP_10037636 BB 235.71720 901.52289
AFFX-SNP_10039349 AB 905.18916 821.52739
AFFX-SNP_10039442 AA 1363.11273 217.90684
AFFX-SNP_10039933 BB 643.97540 1838.50107
AFFX-SNP_10046830 BB 261.87620 1687.83255
AFFX-SNP_10047363 BB 287.81452 853.10194
AFFX-SNP_10047841 AB 836.08416 741.96022
AFFX-SNP_10049334 AB 1870.99869 1348.59443
AFFX-SNP_10052664 BB 287.80790 962.20064
AFFX-SNP_10057887 BB 271.43411 864.26636
AFFX-SNP_10064911 AB 753.56372 823.59981

Total number of rows: 909622

Table truncated, full table size 33725 Kbytes.

Supplementary file Size Download File type/resource
GSM617682_OR1286.CEL.gz 33.4 Mb (ftp)(http) CEL
GSM617682_OR1286.birdseed.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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