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Sample GSM617759 Query DataSets for GSM617759
Status Public on Sep 01, 2011
Title OSCC tumor_OR4058
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 1265.44949 245.12088
AFFX-SNP_10009702 BB 604.10543 830.75061
AFFX-SNP_10015773 BB 1399.01079 2159.88019
AFFX-SNP_10021569 AA 805.39070 494.64758
AFFX-SNP_10026879 BB 735.22386 2124.28682
AFFX-SNP_10029725 BB 402.42639 587.64024
AFFX-SNP_10034687 NoCall 648.91886 1163.13633
AFFX-SNP_10036267 BB 298.83635 879.26715
AFFX-SNP_10037362 BB 948.03556 3862.07207
AFFX-SNP_10037636 BB 220.10691 1289.50994
AFFX-SNP_10039349 BB 338.94268 1317.50109
AFFX-SNP_10039442 AA 1189.84187 172.20139
AFFX-SNP_10039933 BB 631.66777 2046.84074
AFFX-SNP_10046830 AB 956.93345 785.59433
AFFX-SNP_10047363 NoCall 703.82049 373.35129
AFFX-SNP_10047841 BB 633.31188 1146.92709
AFFX-SNP_10049334 AA 2532.00267 916.06423
AFFX-SNP_10052664 BB 330.91480 1088.09104
AFFX-SNP_10057887 AA 680.02147 463.90577
AFFX-SNP_10064911 AA 1123.07747 301.71266

Total number of rows: 909622

Table truncated, full table size 33809 Kbytes.

Supplementary file Size Download File type/resource
GSM617759_OR4058.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM617759_OR4058.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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