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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_104 |
| 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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| |
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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) |
[email protected]
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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 |
0.9801014 |
1.401016 |
1 |
-0.05294114 |
| cnvi0111186 |
NC |
0 |
0 |
0.5262768 |
0 |
0.07965732 |
| cnvi0111187 |
NC |
0 |
0.9872446 |
1.595245 |
1 |
0.06216205 |
| cnvi0111188 |
NC |
0 |
0.005825108 |
1.38007 |
0 |
0.08067728 |
| cnvi0111189 |
NC |
0 |
0.0226669 |
1.580667 |
0 |
0.1322229 |
| cnvi0111190 |
NC |
0 |
0 |
0.3847545 |
0 |
0.1008085 |
| cnvi0111191 |
NC |
0 |
0.02614665 |
0.8264873 |
0 |
-0.4117667 |
| cnvi0111192 |
NC |
0 |
0.01516258 |
1.281123 |
0 |
0.2017495 |
| cnvi0111193 |
NC |
0 |
0.003714692 |
1.154612 |
0 |
-0.07241528 |
| cnvi0111194 |
NC |
0 |
0.9792073 |
1.125844 |
0.9961447 |
-0.2411882 |
| cnvi0111195 |
NC |
0 |
0.02629102 |
2.142069 |
0 |
0.1336134 |
| cnvi0111196 |
NC |
0 |
0.9886219 |
1.147401 |
1 |
-0.09734073 |
| cnvi0111197 |
NC |
0 |
0.002936021 |
1.076403 |
0 |
0.2700135 |
| cnvi0111198 |
NC |
0 |
0.9656379 |
1.181124 |
0.9948499 |
-0.1350614 |
| cnvi0111199 |
NC |
0 |
0.008889091 |
1.380732 |
0 |
0.1188742 |
| cnvi0111200 |
NC |
0 |
0.9886848 |
0.9075615 |
1 |
0.04126201 |
| cnvi0111201 |
NC |
0 |
0.01860251 |
0.8061505 |
0.0001581324 |
-0.1982688 |
| cnvi0111202 |
NC |
0 |
0.9354873 |
1.403772 |
1 |
0.07441764 |
| cnvi0111203 |
NC |
0 |
0.0372111 |
1.98375 |
0.01289678 |
0.2597953 |
| cnvi0111204 |
NC |
0 |
0.9933947 |
1.22177 |
1 |
0.00399735 |
Total number of rows: 299140
Table truncated, full table size 17004 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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