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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_57 |
| 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.
|
| Label |
C-Bio and A-DNP
|
| 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
|
| Street address |
900 E 57th Street
|
| 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 |
0.9810903 |
1.560935 |
1 |
0.1029967 |
| cnvi0111186 |
NC |
0 |
0.01085445 |
0.5769979 |
0 |
0.2124016 |
| cnvi0111187 |
NC |
0 |
0.9900084 |
1.567263 |
1 |
0.03663123 |
| cnvi0111188 |
NC |
0 |
0.008122402 |
1.291408 |
0 |
-0.0151201 |
| cnvi0111189 |
NC |
0 |
0.02410718 |
1.592791 |
0 |
0.1432462 |
| cnvi0111190 |
NC |
0 |
0.006460583 |
0.3645638 |
0 |
0.02304151 |
| cnvi0111191 |
NC |
0 |
0.04658926 |
0.2518252 |
0.01893323 |
-2.126336 |
| cnvi0111192 |
NC |
0 |
0.01124789 |
1.088726 |
0 |
-0.03301883 |
| cnvi0111193 |
NC |
0 |
0.005797841 |
1.194711 |
0 |
-0.02316201 |
| cnvi0111194 |
NC |
0 |
0.9889275 |
1.306934 |
1 |
-0.02600868 |
| cnvi0111195 |
NC |
0 |
0.0324923 |
2.470518 |
0 |
0.3394217 |
| cnvi0111196 |
NC |
0 |
0.9938313 |
1.080392 |
1 |
-0.1841558 |
| cnvi0111197 |
NC |
0 |
0.01107796 |
1.062511 |
0 |
0.2512726 |
| cnvi0111198 |
NC |
0 |
0.9740626 |
1.344129 |
1 |
0.05144942 |
| cnvi0111199 |
NC |
0 |
0.01009856 |
1.465633 |
0 |
0.204965 |
| cnvi0111200 |
NC |
0 |
0.9932901 |
0.8598232 |
1 |
-0.03669328 |
| cnvi0111201 |
NC |
0 |
0.01964494 |
0.8226652 |
0.001247391 |
-0.1690127 |
| cnvi0111202 |
NC |
0 |
0.9449325 |
1.330335 |
1 |
-0.003101398 |
| cnvi0111203 |
NC |
0 |
0.03062998 |
1.751751 |
0.005974192 |
0.08036291 |
| cnvi0111204 |
NC |
0 |
0.9869238 |
1.312416 |
0.9984404 |
0.1072496 |
Total number of rows: 299140
Table truncated, full table size 17100 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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