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Sample GSM617672 Query DataSets for GSM617672
Status Public on Sep 01, 2011
Title OSCC tumor_OR1016
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 704.80674 1714.96670
AFFX-SNP_10009702 AB 1018.81470 691.76187
AFFX-SNP_10015773 BB 1277.41577 2323.36228
AFFX-SNP_10021569 AA 757.63112 389.78454
AFFX-SNP_10026879 BB 763.55292 1863.28415
AFFX-SNP_10029725 AA 800.05273 386.96345
AFFX-SNP_10034687 AA 835.76166 540.49479
AFFX-SNP_10036267 BB 348.33959 884.64048
AFFX-SNP_10037362 BB 1031.95598 3616.52471
AFFX-SNP_10037636 BB 192.43991 799.97579
AFFX-SNP_10039349 BB 324.03256 1159.11933
AFFX-SNP_10039442 AA 1340.96360 181.66655
AFFX-SNP_10039933 BB 777.55171 1708.61438
AFFX-SNP_10046830 AB 639.20486 1310.43897
AFFX-SNP_10047363 AB 637.88666 596.65282
AFFX-SNP_10047841 BB 615.00924 1270.26571
AFFX-SNP_10049334 AA 2702.78910 596.79809
AFFX-SNP_10052664 BB 325.42986 925.10497
AFFX-SNP_10057887 AB 638.58570 627.06667
AFFX-SNP_10064911 AB 708.45012 725.71067

Total number of rows: 909622

Table truncated, full table size 33720 Kbytes.

Supplementary file Size Download File type/resource
GSM617672_OR1016.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM617672_OR1016.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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