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Sample GSM195015 Query DataSets for GSM195015
Status Public on May 30, 2007
Title Frozen rectal tumor sample (B598)
Sample type genomic
 
Source name Frozen rectal tumor sample (B598)
Organism Homo sapiens
Characteristics gender: F
gender: 50
tissue: rectal carcinoma
tumor stage: T2N0
Treatment protocol n.a.
Growth protocol n.a.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated with the Genomic Wizard Kit (Promega)
Label biotin
Label protocol Biotinylated DNA wase prepared according to the standard Affymetrix protocol for Affymetrix 10K SNP arrays
 
Hybridization protocol Hybridisation according to the protocol for Affymetrix 10K SNP arrays
Scan protocol GeneChips were scanned using the GeneChip® Scanner 3000
Description test
Data processing Genotypes were scored with the GDAS software (Affymetrix). Copy numbers were consequently computed with dCHIP SNP and CNAG. Samples were normalized against a set of in-house normal reference samples.
 
Submission date May 29, 2007
Last update date May 29, 2007
Contact name Esther Lips
E-mail(s) e.lips@nki.nl
Phone +31-20-5122039
Organization name NKI-AVL
Department Molecular Pathology
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platform ID GPL2641
Series (2)
GSE7946 SNP array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas
GSE12225 Integrating chromosomal aberrations and gene expression profiles to dissect rectal cancer

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 7518.5 0 0 0 0 0 0
AFFX-5Q-456 No Call 2867.5 0 0 0 0 0 0
AFFX-5Q-789 No Call 9480 0 0 0 0 0 0
AFFX-5Q-ABC No Call 9852.5 0 0 0 0 0 0
SNP_A-1513509 AB 0.638188 0.433333 0.35567 0.433333 0.35567 0 0
SNP_A-1518411 BB 0.103759 0.0620915 0.0566038 0.0620915 0.0566038 0 0
SNP_A-1511066 AB 0.361263 0.566265 0.539463 0.566265 0.539463 0 0
SNP_A-1517367 AA 0.0645771 1 0.957565 1 0.957565 0 0
SNP_A-1512567 BB 0.143936 0.0604435 0.174272 0.0604435 0.174272 0 0
SNP_A-1519604 AA 0.360885 0.748856 0.881135 0.748856 0.881135 0 0
SNP_A-1507932 AB 0.239091 0.521333 0.49228 0.521333 0.49228 0 0
SNP_A-1519685 No Call 0.877839 0.401035 0.198321 0.401035 0.198321 0 0
SNP_A-1516165 AA 0.15119 1 0.965794 1 0.965794 0 0
SNP_A-1514890 BB 0.195206 0.130556 0.126219 0.130556 0.126219 0 0
SNP_A-1507580 BB 0.0824978 0.132111 0 0.132111 0 0 0
SNP_A-1510991 AB 0.473228 0.393728 0.296088 0.393728 0.296088 0 0
SNP_A-1516205 AA 0.125184 0.97795 0.879913 0.97795 0.879913 0 0
SNP_A-1512666 BB 0 0 0 0 0 0 0
SNP_A-1512740 BB 0.146287 0.187427 0 0.187427 0 0 0
SNP_A-1512132 AA 0.237684 0.997708 0.966587 0.997708 0.966587 0 0

Total number of rows: 10208

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM195015.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM195015.CHP.gz 107.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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