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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_101 |
| 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 |
0.9826696 |
1.292519 |
1 |
-0.1692286 |
| cnvi0111186 |
NC |
0 |
0 |
0.6118429 |
0 |
0.2969967 |
| cnvi0111187 |
NC |
0 |
0.9830302 |
1.608037 |
0.9977963 |
0.07368387 |
| cnvi0111188 |
NC |
0 |
0.009345911 |
1.379048 |
0 |
0.07960853 |
| cnvi0111189 |
NC |
0 |
0.02217072 |
1.530884 |
0 |
0.08605364 |
| cnvi0111190 |
NC |
0 |
0 |
0.49134 |
0 |
0.4535919 |
| cnvi0111191 |
NC |
0 |
0.01834573 |
1.229809 |
0 |
0.1616033 |
| cnvi0111192 |
NC |
0 |
0.01194896 |
1.09555 |
0 |
-0.0240033 |
| cnvi0111193 |
NC |
0 |
0.005411404 |
1.193848 |
0 |
-0.02420447 |
| cnvi0111194 |
NC |
0 |
0.989091 |
1.210771 |
1 |
-0.1362684 |
| cnvi0111195 |
NC |
0 |
0.02440619 |
2.150833 |
0 |
0.1395037 |
| cnvi0111196 |
NC |
0 |
0.9916726 |
1.107925 |
1 |
-0.1478501 |
| cnvi0111197 |
NC |
0 |
0.003613255 |
1.05645 |
0 |
0.2430193 |
| cnvi0111198 |
NC |
0 |
0.9779778 |
1.277186 |
1 |
-0.02225294 |
| cnvi0111199 |
NC |
0 |
0.008312435 |
1.49252 |
0 |
0.231191 |
| cnvi0111200 |
NC |
0 |
0.9925944 |
0.9062178 |
1 |
0.03912439 |
| cnvi0111201 |
NC |
0 |
0.01506022 |
0.7539836 |
0 |
-0.2947848 |
| cnvi0111202 |
NC |
0 |
0.9419593 |
1.392857 |
1 |
0.0631566 |
| cnvi0111203 |
NC |
0 |
0.0404733 |
1.918189 |
0.01632824 |
0.2113102 |
| cnvi0111204 |
NC |
0 |
0.9876552 |
1.256803 |
0.9991993 |
0.04478272 |
Total number of rows: 299140
Table truncated, full table size 17001 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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