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Sample GSM617665 Query DataSets for GSM617665
Status Public on Sep 01, 2011
Title OSCC tumor_OR0923
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 978.77553 366.14420
AFFX-SNP_10009702 BB 264.57501 816.30011
AFFX-SNP_10015773 BB 1163.44111 1971.94453
AFFX-SNP_10021569 AA 804.48578 388.74710
AFFX-SNP_10026879 BB 706.67182 1791.91192
AFFX-SNP_10029725 BB 371.22128 629.54502
AFFX-SNP_10034687 AA 1039.43376 410.54683
AFFX-SNP_10036267 BB 324.96377 844.66871
AFFX-SNP_10037362 BB 838.17485 3429.46862
AFFX-SNP_10037636 BB 207.93318 890.83656
AFFX-SNP_10039349 AB 936.39604 748.30809
AFFX-SNP_10039442 AA 1493.96684 163.91107
AFFX-SNP_10039933 BB 652.42444 1859.51101
AFFX-SNP_10046830 BB 270.42897 2003.59710
AFFX-SNP_10047363 BB 332.69182 826.26248
AFFX-SNP_10047841 AB 742.64244 880.90164
AFFX-SNP_10049334 AB 1777.51770 1285.67328
AFFX-SNP_10052664 AB 668.96927 708.62610
AFFX-SNP_10057887 AA 838.62086 431.06541
AFFX-SNP_10064911 AA 956.41275 269.83698

Total number of rows: 909622

Table truncated, full table size 33716 Kbytes.

Supplementary file Size Download File type/resource
GSM617665_OR0923.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM617665_OR0923.birdseed.chp.gz 13.0 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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