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Sample GSM617714 Query DataSets for GSM617714
Status Public on Sep 01, 2011
Title OSCC tumor_OR2442
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 1250.34164 248.55072
AFFX-SNP_10009702 AB 927.81275 558.09320
AFFX-SNP_10015773 AA 2028.81208 964.17208
AFFX-SNP_10021569 AA 727.21451 407.69218
AFFX-SNP_10026879 BB 730.89082 1989.89213
AFFX-SNP_10029725 AB 494.65274 450.13788
AFFX-SNP_10034687 AB 762.49611 1026.16080
AFFX-SNP_10036267 BB 346.06951 773.16939
AFFX-SNP_10037362 BB 1089.29659 3883.54193
AFFX-SNP_10037636 BB 192.18704 937.20500
AFFX-SNP_10039349 AB 847.06996 696.83503
AFFX-SNP_10039442 AA 1419.59651 182.35419
AFFX-SNP_10039933 BB 761.85331 1904.97047
AFFX-SNP_10046830 AA 1238.63788 292.79713
AFFX-SNP_10047363 BB 419.34508 901.78329
AFFX-SNP_10047841 BB 733.46282 1271.27468
AFFX-SNP_10049334 AB 1838.57796 1745.94439
AFFX-SNP_10052664 BB 326.43288 878.62158
AFFX-SNP_10057887 AB 486.96642 638.95562
AFFX-SNP_10064911 AA 878.51022 278.79714

Total number of rows: 909622

Table truncated, full table size 33742 Kbytes.

Supplementary file Size Download File type/resource
GSM617714_OR2442.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617714_OR2442.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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