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Sample GSM288860 Query DataSets for GSM288860
Status Public on Nov 01, 2008
Title MC22
Sample type genomic
 
Source Name Renal Neoplasm, Unclassified, DNA from Paraffin Embedded Tissue
Organism(s) Homo sapiens
Characteristics Sex:M
AgeDecade:60-69
Tumor Size:10
Furhman Nuclear Grade:3
TNM Stage:T2 Nx Mx
LymphoVascular Invasion:N
Extracted molecule genomic DNA
Extraction protocol Deparaffinization followed by Qiagen DNaasy Mini kit by manufacturer's instructions
Label Biotinilated - Fragmented PCR products
Label protocol Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)
 
Hybridization protocol Affymetrix Mapping 10K Xba 2.0 Assay
Scan protocol Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner
Description RenalTumor_Unclassified_FFPE_15
Data processing Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0
 
Submission date May 14, 2008
Contact name Federico A Monzon
E-mail(s) famonzon@tmhs.org
Organization name The Methodist Hospital Research Institute
Department Pathology
Street address 6565 Fannin St., MS205
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL2641
Series (1)
GSE11447 Diagnosis of Morphologically Challenging Cases of Renal Epithelial Neoplasms by Virtual Karyotypes with SNP Arrays

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 16035 0 0 0 0 0 0
AFFX-5Q-456 No Call 5579.5 0 0 0 0 0 0
AFFX-5Q-789 No Call 19728 0 0 0 0 0 0
AFFX-5Q-ABC No Call 22796 0 0 0 0 0 0
SNP_A-1513509 AB 0.238172 0.555714 0.549745 0.555714 0.549745 0 0
SNP_A-1518411 BB 0.192394 0 0.0103383 0 0.0103383 0 0
SNP_A-1511066 No Call 1.45977 0.353349 0.385832 0.353349 0.385832 0 0
SNP_A-1517367 AA 0.19986 0.978508 0.852538 0.978508 0.852538 0 0
SNP_A-1512567 BB 0.238237 0.0718358 0.0899601 0.0718358 0.0899601 0 0
SNP_A-1519604 BB 0.224586 0 0.0110594 0 0.0110594 0 0
SNP_A-1507932 BB 0.287172 0.100244 0.0431034 0.100244 0.0431034 0 0
SNP_A-1519685 AB 0.776951 0.512173 0.38664 0.512173 0.38664 0 0
SNP_A-1516165 BB 0.208945 0 0 0 0 0 0
SNP_A-1514890 AA 0.462736 0.618445 0.886905 0.618445 0.886905 0 0
SNP_A-1507580 BB 0.137501 0.0759312 0.003996 0.0759312 0.003996 0 0
SNP_A-1510991 AB 0.264276 0.45529 0.462424 0.45529 0.462424 0 0
SNP_A-1516205 No Call 10 -2 -2 -2 -2 0 0
SNP_A-1512666 No Call 10 -2 -2 -2 -2 0 0
SNP_A-1512740 BB 0.172338 0.102003 0.0636994 0.102003 0.0636994 0 0
SNP_A-1512132 AA 0.156389 0.903372 0.979726 0.903372 0.979726 0 0

Total number of rows: 10208

Table truncated, full table size 585 Kbytes.




Supplementary file Size Download File type/resource
GSM288860.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM288860.CHP.gz 106.3 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file
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