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Sample GSM617752 Query DataSets for GSM617752
Status Public on Sep 01, 2011
Title OSCC tumor_OR4003
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 1083.20244 212.03812
AFFX-SNP_10009702 AB 1077.85943 544.44950
AFFX-SNP_10015773 AB 1563.81738 1449.25432
AFFX-SNP_10021569 AB 593.48360 690.85966
AFFX-SNP_10026879 BB 628.07819 1817.15321
AFFX-SNP_10029725 AB 667.27648 465.08412
AFFX-SNP_10034687 AB 857.29019 796.53923
AFFX-SNP_10036267 AB 491.68018 619.40484
AFFX-SNP_10037362 AB 2550.11899 2484.12108
AFFX-SNP_10037636 BB 229.71647 872.07258
AFFX-SNP_10039349 BB 279.85839 1188.12601
AFFX-SNP_10039442 AA 1580.55277 234.74924
AFFX-SNP_10039933 BB 745.54367 1940.36934
AFFX-SNP_10046830 AA 1407.07387 267.96435
AFFX-SNP_10047363 AB 490.35733 459.39326
AFFX-SNP_10047841 AB 802.41943 822.32171
AFFX-SNP_10049334 BB 473.07161 2032.77713
AFFX-SNP_10052664 BB 286.88224 1106.61922
AFFX-SNP_10057887 BB 226.93472 954.10169
AFFX-SNP_10064911 AA 947.40882 317.23571

Total number of rows: 909622

Table truncated, full table size 33727 Kbytes.

Supplementary file Size Download File type/resource
GSM617752_OR4003.CEL.gz 32.9 Mb (ftp)(http) CEL
GSM617752_OR4003.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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