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Sample GSM523634 Query DataSets for GSM523634
Status Public on Mar 18, 2010
Title Tumor_9nsp
Sample type genomic
 
Source name head and neck tumor_9
Organism Homo sapiens
Characteristics tissue: head and neck squamous cell carcinoma
tumor site: oral
tumor id: 106
Treatment protocol None.
Growth protocol Fresh-frozen human tissue.
Extracted molecule genomic DNA
Extraction protocol Qiagen Qiamp DNA extraction kit.
Label biotin
Label protocol As per manufacturer (Affymetrix).
 
Hybridization protocol As per manufacturer (Affymetrix).
Scan protocol As per manufacturer (Affymetrix).
Description Tumor ID 106
Hybridized to 250K_Nsp.
Data processing Data were collected at the Harvard Partners Microarray Core Facility. Inferred copy number states of each SNP were extracted and converted from .CEL files into signal intensities using GCOS and Affymetrix Copy Number Analysis Tool (CNAT) v4.0.1. We utilized the HMM-based algorithm with defaults for tuning parameters, Gaussian smoothing, transition decay, and median scaling.

The 'GSE20939_tumor_copy_number.txt' file, which is linked to the Series GSE20939 record as a supplementary file, contains the (blood-adjusted) tumor copy number calls used in our final analyses.
 
Submission date Mar 17, 2010
Last update date Nov 02, 2010
Contact name Graham M Poage
Organization name Brown University
Street address 70 Ship St
City Providence
State/province RI
ZIP/Postal code 02903
Country USA
 
Platform ID GPL3718
Series (1)
GSE20939 Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (Affymetrix Copy Number)

Data table header descriptions
ID_REF
VALUE Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1 Relative allele signal for the data in the first probe group
RAS2 Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF VALUE CONFIDENCE RAS1 RAS2 P-VALUE AA P-VALUE AB P-VALUE BB P-VALUE NO CALL
AFFX-5Q-123 No Call 0 0 0 0 0 0 0
AFFX-5Q-456 No Call 0 0 0 0 0 0 0
AFFX-5Q-789 No Call 0 0 0 0 0 0 0
AFFX-5Q-ABC No Call 0 0 0 0 0 0 0
AFFX-barcodeA No Call 0 0 0 0 0 0 0
AFFX-barcodeB No Call 0 0 0 0 0 0 0
AFFX-barcodeC No Call 0 0 0 0 0 0 0
AFFX-barcodeD No Call 0 0 0 0 0 0 0
AFFX-barcodeE No Call 0 0 0 0 0 0 0
AFFX-barcodeF No Call 0 0 0 0 0 0 0
AFFX-barcodeG No Call 0 0 0 0 0 0 0
AFFX-barcodeH No Call 0 0 0 0 0 0 0
AFFX-barcodeI No Call 0 0 0 0 0 0 0
AFFX-barcodeJ No Call 0 0 0 0 0 0 0
AFFX-barcodeK No Call 0 0 0 0 0 0 0
AFFX-barcodeL No Call 0 0 0 0 0 0 0
AFFX-barcodeM No Call 0 0 0 0 0 0 0
AFFX-barcodeN No Call 0 0 0 0 0 0 0
AFFX-barcodeO No Call 0 0 0 0 0 0 0
AFFX-barcodeP No Call 0 0 0 0 0 0 0

Total number of rows: 262338

Table truncated, full table size 19980 Kbytes.




Supplementary file Size Download File type/resource
GSM523634.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM523634.CHP.gz 693.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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