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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_59 |
| 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
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| 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 |
0.9749403 |
1.704718 |
1 |
0.2301187 |
| cnvi0111186 |
NC |
0 |
0.005877678 |
0.5382676 |
0 |
0.1121589 |
| cnvi0111187 |
NC |
0 |
0.9851524 |
1.400964 |
1 |
-0.1251966 |
| cnvi0111188 |
NC |
0 |
0.01049552 |
1.330887 |
0 |
0.02832327 |
| cnvi0111189 |
NC |
0 |
0.02234746 |
1.440328 |
0 |
-0.00191399 |
| cnvi0111190 |
NC |
0 |
0 |
0.5532405 |
0 |
0.624777 |
| cnvi0111191 |
NC |
0 |
0.02996619 |
1.055779 |
0.001380904 |
-0.05852308 |
| cnvi0111192 |
NC |
0 |
0.01548671 |
1.148613 |
0 |
0.04423419 |
| cnvi0111193 |
NC |
0 |
0.005439965 |
1.258222 |
0 |
0.05156254 |
| cnvi0111194 |
NC |
0 |
0.9898525 |
1.32334 |
1 |
-0.008010999 |
| cnvi0111195 |
NC |
0 |
0.0309383 |
2.224973 |
0 |
0.1883961 |
| cnvi0111196 |
NC |
0 |
0.9864312 |
1.071836 |
1 |
-0.1956254 |
| cnvi0111197 |
NC |
0 |
0.005925576 |
0.963338 |
0 |
0.1099088 |
| cnvi0111198 |
NC |
0 |
0.9665637 |
1.363539 |
0.9958283 |
0.07213443 |
| cnvi0111199 |
NC |
0 |
0.006531325 |
1.344516 |
0 |
0.08052727 |
| cnvi0111200 |
NC |
0 |
0.9929233 |
0.9077704 |
1 |
0.04159407 |
| cnvi0111201 |
NC |
0 |
0.01487615 |
0.8424613 |
0 |
-0.1347076 |
| cnvi0111202 |
NC |
0 |
0.9417465 |
1.345002 |
1 |
0.01271763 |
| cnvi0111203 |
NC |
0 |
0.03656487 |
1.835341 |
0.01221702 |
0.1476135 |
| cnvi0111204 |
NC |
0 |
0.9877536 |
1.385428 |
0.9993015 |
0.1853557 |
Total number of rows: 299140
Table truncated, full table size 17164 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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