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Sample GSM617762 Query DataSets for GSM617762
Status Public on Sep 01, 2011
Title OSCC tumor_OR4081
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 646.77087 1487.15217
AFFX-SNP_10009702 AA 1299.45778 312.67158
AFFX-SNP_10015773 AB 1538.68229 1596.26128
AFFX-SNP_10021569 AA 796.00565 439.52383
AFFX-SNP_10026879 BB 529.77151 1680.28673
AFFX-SNP_10029725 AB 574.90586 446.68660
AFFX-SNP_10034687 AA 1535.20920 421.12388
AFFX-SNP_10036267 AB 430.12407 575.55876
AFFX-SNP_10037362 BB 1010.57687 3420.21829
AFFX-SNP_10037636 BB 155.33196 983.01434
AFFX-SNP_10039349 BB 307.98176 1005.98085
AFFX-SNP_10039442 AA 1442.91162 175.16749
AFFX-SNP_10039933 BB 811.34288 2008.29567
AFFX-SNP_10046830 AB 730.65209 972.49084
AFFX-SNP_10047363 AB 509.03078 368.17088
AFFX-SNP_10047841 AB 831.40837 804.88037
AFFX-SNP_10049334 AB 1703.91653 1276.58180
AFFX-SNP_10052664 BB 295.04911 1128.92941
AFFX-SNP_10057887 AB 501.60232 629.30545
AFFX-SNP_10064911 AB 658.66202 634.65091

Total number of rows: 909622

Table truncated, full table size 33748 Kbytes.

Supplementary file Size Download File type/resource
GSM617762_OR4081.CEL.gz 33.2 Mb (ftp)(http) CEL
GSM617762_OR4081.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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