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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_53 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, tumor
|
| 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 |
| |
|
| 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 |
0.9713144 |
1.295599 |
0.9962885 |
-0.1657951 |
| cnvi0111186 |
NC |
0 |
0.02627528 |
0.3022601 |
0 |
-0.7203742 |
| cnvi0111187 |
NC |
0 |
0.9861159 |
1.370163 |
1 |
-0.1572688 |
| cnvi0111188 |
NC |
0 |
0.0100025 |
1.487682 |
0 |
0.1890018 |
| cnvi0111189 |
NC |
0 |
0.02797993 |
1.406681 |
0.001721835 |
-0.03601576 |
| cnvi0111190 |
NC |
0 |
0 |
0.4228654 |
0 |
0.2370688 |
| cnvi0111191 |
NC |
0 |
0.03799381 |
0.7864276 |
0.009857285 |
-0.4834454 |
| cnvi0111192 |
NC |
0 |
0.02115268 |
1.419557 |
0 |
0.349782 |
| cnvi0111193 |
NC |
0 |
0.009195094 |
0.3582038 |
0 |
-1.760971 |
| cnvi0111194 |
NC |
0 |
0.9828674 |
1.464339 |
0.9999638 |
0.138055 |
| cnvi0111195 |
NC |
0 |
0.03738624 |
2.800454 |
0.005122587 |
0.5202693 |
| cnvi0111196 |
NC |
0 |
0.9846752 |
1.203666 |
1 |
-0.02827471 |
| cnvi0111197 |
NC |
0 |
0.009738921 |
0.9900016 |
0 |
0.1492976 |
| cnvi0111198 |
NC |
0 |
0.9686185 |
1.425443 |
0.9979998 |
0.136188 |
| cnvi0111199 |
NC |
0 |
0.01205545 |
1.974791 |
0 |
0.6351409 |
| cnvi0111200 |
NC |
0 |
0.9965423 |
0.8223453 |
1 |
-0.1009891 |
| cnvi0111201 |
NC |
0 |
0.02915609 |
0.782353 |
0.01118579 |
-0.2414984 |
| cnvi0111202 |
NC |
0 |
0.9329367 |
1.582226 |
1 |
0.2470651 |
| cnvi0111203 |
NC |
0 |
0.02892551 |
0.8258334 |
0.004181277 |
-1.004512 |
| cnvi0111204 |
NC |
0 |
0.9797359 |
1.354784 |
0.9909819 |
0.1530875 |
Total number of rows: 299140
Table truncated, full table size 17307 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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