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Sample GSM617750 Query DataSets for GSM617750
Status Public on Sep 01, 2011
Title OSCC tumor_OR3383
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 652.08954 1453.51409
AFFX-SNP_10009702 AB 781.68095 736.20185
AFFX-SNP_10015773 BB 1172.44782 1785.02408
AFFX-SNP_10021569 AA 802.74507 442.81494
AFFX-SNP_10026879 BB 555.18536 1841.07132
AFFX-SNP_10029725 AB 505.47402 418.43946
AFFX-SNP_10034687 AA 1034.18703 362.33792
AFFX-SNP_10036267 BB 279.64780 804.77421
AFFX-SNP_10037362 BB 813.87705 3393.24877
AFFX-SNP_10037636 BB 192.59256 1028.17324
AFFX-SNP_10039349 AB 874.11843 789.35267
AFFX-SNP_10039442 AA 1373.80806 191.59226
AFFX-SNP_10039933 BB 629.53315 1855.57272
AFFX-SNP_10046830 AB 899.56175 1186.59190
AFFX-SNP_10047363 AB 505.81975 464.94335
AFFX-SNP_10047841 AA 853.45556 333.05836
AFFX-SNP_10049334 BB 440.75124 1659.72709
AFFX-SNP_10052664 BB 295.11047 966.94830
AFFX-SNP_10057887 BB 216.59542 780.17007
AFFX-SNP_10064911 BB 352.84698 970.55160

Total number of rows: 909622

Table truncated, full table size 33730 Kbytes.

Supplementary file Size Download File type/resource
GSM617750_OR3383.CEL.gz 33.4 Mb (ftp)(http) CEL
GSM617750_OR3383.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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