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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 19, 2014 |
| Title |
Colon Tissue Sample_68 |
| Sample type |
genomic |
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| Source name |
Colon tissue, tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| Label |
C-Bio and A-DNP
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| Label protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.
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| Hybridization protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.
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| Scan protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using the Illumina BeadArray scanner.
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| Data processing |
Illumina BeadStudio v3.3.4 normalized intensity values and BAF data were imported into PARTEK Genomics Suite for statistical analysis.
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| Submission date |
Dec 23, 2011 |
| Last update date |
Dec 19, 2014 |
| Contact name |
Muhammad Ghulam Kibriya |
| E-mail(s) |
kibriya@uchicago.edu
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| Organization name |
The University of Chicago
|
| Department |
Health Studies
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| Street address |
900 E 57th Street
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| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL13829 |
| Series (1) |
| GSE34678 |
A Genome-wide Study of Cytogenetic Changes in Colorectal Cancer Using SNP Microarrays: Possibilities for Future Personalized Treatment |
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| Data table header descriptions |
| ID_REF |
|
| VALUE |
Genotype: AA, AB, BB, or NC (no call) |
| Score |
Score |
| Theta |
Theta |
| R |
R |
| B Allele Freq |
BAF |
| Log R Ratio |
Log R Ratio |
| Data table |
| ID_REF |
VALUE |
Score |
Theta |
R |
B Allele Freq |
Log R Ratio |
| cnvi0111185 |
NC |
0 |
0.9767302 |
1.498152 |
1 |
0.04376971 |
| cnvi0111186 |
NC |
0 |
0.008558855 |
0.5128107 |
0 |
0.04226183 |
| cnvi0111187 |
NC |
0 |
0.9864312 |
1.663473 |
1 |
0.1225821 |
| cnvi0111188 |
NC |
0 |
0.007846208 |
1.313131 |
0 |
0.00894605 |
| cnvi0111189 |
NC |
0 |
0.02128561 |
1.509435 |
0 |
0.06569778 |
| cnvi0111190 |
NC |
0 |
0 |
0.3329313 |
0 |
-0.1079052 |
| cnvi0111191 |
NC |
0 |
0.03816856 |
0.5285522 |
0.01004179 |
-1.056713 |
| cnvi0111192 |
NC |
0 |
0.01695498 |
1.09125 |
0 |
-0.02967697 |
| cnvi0111193 |
NC |
0 |
0.00569322 |
1.107359 |
0 |
-0.1327004 |
| cnvi0111194 |
NC |
0 |
0.9904717 |
1.120244 |
1 |
-0.2483814 |
| cnvi0111195 |
NC |
0 |
0.03416643 |
2.215314 |
0.00170909 |
0.1821195 |
| cnvi0111196 |
NC |
0 |
0.986634 |
1.176616 |
1 |
-0.06106629 |
| cnvi0111197 |
NC |
0 |
0.009766291 |
0.7865825 |
0 |
-0.1825352 |
| cnvi0111198 |
NC |
0 |
0.970793 |
1.324108 |
1 |
0.02979891 |
| cnvi0111199 |
NC |
0 |
0.00845741 |
1.332983 |
0 |
0.06809922 |
| cnvi0111200 |
NC |
0 |
0.991336 |
0.9229479 |
1 |
0.06551591 |
| cnvi0111201 |
NC |
0 |
0.01552212 |
0.8198122 |
0 |
-0.1740245 |
| cnvi0111202 |
NC |
0 |
0.9434866 |
1.229401 |
1 |
-0.1169358 |
| cnvi0111203 |
NC |
0 |
0.04765511 |
2.134656 |
0.02388269 |
0.365569 |
| cnvi0111204 |
NC |
0 |
0.9925855 |
1.28583 |
1 |
0.07772449 |
Total number of rows: 299140
Table truncated, full table size 17104 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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