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Sample GSM617685 Query DataSets for GSM617685
Status Public on Sep 01, 2011
Title OSCC tumor_OR1320
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 793.73375 1523.02993
AFFX-SNP_10009702 BB 289.47124 823.33253
AFFX-SNP_10015773 AA 1932.99970 895.42935
AFFX-SNP_10021569 AA 793.38811 344.01192
AFFX-SNP_10026879 AB 1441.42608 1501.94873
AFFX-SNP_10029725 BB 371.03200 595.28039
AFFX-SNP_10034687 BB 347.45474 1082.39154
AFFX-SNP_10036267 BB 327.56077 767.01875
AFFX-SNP_10037362 BB 1049.28132 3679.88884
AFFX-SNP_10037636 BB 226.59403 891.06080
AFFX-SNP_10039349 AB 916.62034 715.63494
AFFX-SNP_10039442 AA 1644.52818 212.19792
AFFX-SNP_10039933 BB 763.03528 1990.68422
AFFX-SNP_10046830 BB 314.07232 1741.73418
AFFX-SNP_10047363 AB 679.32398 463.62098
AFFX-SNP_10047841 AB 941.43945 963.12554
AFFX-SNP_10049334 AA 2600.92358 513.08544
AFFX-SNP_10052664 BB 265.22569 1004.48629
AFFX-SNP_10057887 AB 531.26984 590.14551
AFFX-SNP_10064911 AB 646.86484 770.32225

Total number of rows: 909622

Table truncated, full table size 33720 Kbytes.

Supplementary file Size Download File type/resource
GSM617685_OR1320.CEL.gz 33.5 Mb (ftp)(http) CEL
GSM617685_OR1320.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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