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Sample GSM617701 Query DataSets for GSM617701
Status Public on Sep 01, 2011
Title OSCC tumor_OR2231
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 BB 334.71457 2360.76579
AFFX-SNP_10009702 AA 1421.41729 282.54273
AFFX-SNP_10015773 AB 1742.37111 1541.84790
AFFX-SNP_10021569 AA 685.59599 385.01447
AFFX-SNP_10026879 AB 1413.00292 1418.82325
AFFX-SNP_10029725 AB 594.61958 438.76543
AFFX-SNP_10034687 AA 1083.63794 447.74774
AFFX-SNP_10036267 AB 428.66547 467.05950
AFFX-SNP_10037362 BB 1081.00760 3790.44563
AFFX-SNP_10037636 BB 189.99990 895.08674
AFFX-SNP_10039349 BB 251.74406 1005.03398
AFFX-SNP_10039442 AA 1426.18727 168.84686
AFFX-SNP_10039933 BB 864.13280 2045.99514
AFFX-SNP_10046830 BB 247.15735 1939.55006
AFFX-SNP_10047363 AB 512.28554 423.28219
AFFX-SNP_10047841 AB 977.85742 700.73180
AFFX-SNP_10049334 AA 3036.60757 477.75920
AFFX-SNP_10052664 BB 291.83477 927.53616
AFFX-SNP_10057887 AA 718.09313 329.17363
AFFX-SNP_10064911 AB 666.37863 649.35386

Total number of rows: 909622

Table truncated, full table size 33739 Kbytes.

Supplementary file Size Download File type/resource
GSM617701_OR2231.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM617701_OR2231.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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