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| Status |
Public on Nov 01, 2008 |
| Title |
CUMC06 |
| Sample type |
genomic |
| |
|
| Source name |
Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sex: M
agedecade: 50-59
tumor size: 5.5
furhman nuclear grade: 3
tnm stage: T1bNxMx
lymphovascular invasion: N
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Deparaffinization followed by Qiagen DNaasy Mini kit by manufacturer's instructions
|
| Label |
Biotin
|
| 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
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| Description |
RenalCellCarcinoma_ClearCell_FFPE_Rep11
|
| Data processing |
Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0
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| |
|
| Submission date |
Sep 03, 2009 |
| Last update date |
Sep 03, 2009 |
| 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 (3) |
| GSE11447 |
Diagnosis of Morphologically Challenging Cases of Renal Epithelial Neoplasms by Virtual Karyotypes with SNP Arrays |
| GSE12808 |
Detection of chromosomal aberrations in renal tumors by virtual karyotyping with SNP microarrays |
| GSE14670 |
Virtual-Karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms |
|
| 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 |
11193 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-456 |
No Call |
5295.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-789 |
No Call |
16042.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-ABC |
No Call |
17306.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| SNP_A-1513509 |
BB |
0.0491611 |
0.0169964 |
0 |
0.0169964 |
0 |
0 |
0 |
| SNP_A-1518411 |
AB |
0.130768 |
0.526174 |
0.531627 |
0.526174 |
0.531627 |
0 |
0 |
| SNP_A-1511066 |
AA |
0.0807614 |
1 |
0.876832 |
1 |
0.876832 |
0 |
0 |
| SNP_A-1517367 |
AA |
0.128394 |
0.937443 |
0.926591 |
0.937443 |
0.926591 |
0 |
0 |
| SNP_A-1512567 |
AA |
0.609345 |
0.474986 |
0.708555 |
0.474986 |
0.708555 |
0 |
0 |
| SNP_A-1519604 |
AA |
0.216062 |
0.825545 |
1 |
0.825545 |
1 |
0 |
0 |
| SNP_A-1507932 |
AB |
0.633097 |
0.449013 |
0.313131 |
0.449013 |
0.313131 |
0 |
0 |
| SNP_A-1519685 |
AB |
0.287823 |
0.640841 |
0.457106 |
0.640841 |
0.457106 |
0 |
0 |
| SNP_A-1516165 |
AA |
0.271684 |
1 |
0.938533 |
1 |
0.938533 |
0 |
0 |
| SNP_A-1514890 |
BB |
0.716422 |
0.211386 |
0.223871 |
0.211386 |
0.223871 |
0 |
0 |
| SNP_A-1507580 |
No Call |
1.09187 |
0.405624 |
0.0764873 |
0.405624 |
0.0764873 |
0 |
0 |
| SNP_A-1510991 |
AA |
0.0976435 |
0.98523 |
0.897662 |
0.98523 |
0.897662 |
0 |
0 |
| SNP_A-1516205 |
AA |
0.482095 |
1 |
0.777547 |
1 |
0.777547 |
0 |
0 |
| SNP_A-1512666 |
No Call |
0.821749 |
0 |
0.273435 |
0 |
0.273435 |
0 |
0 |
| SNP_A-1512740 |
BB |
0.305548 |
0.0857143 |
0.121394 |
0.0857143 |
0.121394 |
0 |
0 |
| SNP_A-1512132 |
AA |
0.12986 |
0.917334 |
0.954603 |
0.917334 |
0.954603 |
0 |
0 |
Total number of rows: 10208
Table truncated, full table size 608 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM288829.CEL.gz |
2.0 Mb |
(ftp)(http) |
CEL |
| GSM288829.CHP.gz |
112.6 Kb |
(ftp)(http) |
CHP |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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