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Sample GSM617710 Query DataSets for GSM617710
Status Public on Sep 01, 2011
Title OSCC tumor_OR2348
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 AB 667.37779 1482.96201
AFFX-SNP_10009702 AA 1282.40525 244.87351
AFFX-SNP_10015773 AA 1716.20713 954.91822
AFFX-SNP_10021569 AA 648.82974 379.77846
AFFX-SNP_10026879 BB 715.11188 1956.09650
AFFX-SNP_10029725 AB 574.76144 465.14652
AFFX-SNP_10034687 AA 1036.34005 407.77791
AFFX-SNP_10036267 BB 364.86136 867.27978
AFFX-SNP_10037362 BB 967.47545 3483.98414
AFFX-SNP_10037636 BB 272.47165 814.75130
AFFX-SNP_10039349 BB 295.56145 1025.47287
AFFX-SNP_10039442 AA 1476.00995 225.30091
AFFX-SNP_10039933 BB 693.76510 2062.64586
AFFX-SNP_10046830 AB 725.48750 1157.43636
AFFX-SNP_10047363 AA 697.81176 205.91200
AFFX-SNP_10047841 AA 1251.31449 414.12980
AFFX-SNP_10049334 AB 1813.85403 1254.33380
AFFX-SNP_10052664 BB 336.19921 1002.24666
AFFX-SNP_10057887 AA 855.50531 427.39299
AFFX-SNP_10064911 AB 616.62807 616.59634

Total number of rows: 909622

Table truncated, full table size 33730 Kbytes.

Supplementary file Size Download File type/resource
GSM617710_OR2348.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM617710_OR2348.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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