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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_84 |
| 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 |
0.978687 |
1.452427 |
1 |
-0.0009483933 |
| cnvi0111186 |
NC |
0 |
0.008901316 |
0.5460514 |
0 |
0.1328722 |
| cnvi0111187 |
NC |
0 |
0.9897224 |
1.515566 |
1 |
-0.01175928 |
| cnvi0111188 |
NC |
0 |
0.009864689 |
1.356542 |
0 |
0.05586869 |
| cnvi0111189 |
NC |
0 |
0.0229088 |
1.479529 |
0 |
0.03682674 |
| cnvi0111190 |
NC |
0 |
0.002746083 |
0.4743047 |
0 |
0.4026843 |
| cnvi0111191 |
NC |
0 |
0.02859269 |
1.164959 |
0 |
0.08344816 |
| cnvi0111192 |
NC |
0 |
0.02018431 |
1.143307 |
0 |
0.03755318 |
| cnvi0111193 |
NC |
0 |
0.007048726 |
1.24304 |
0 |
0.03404833 |
| cnvi0111194 |
NC |
0 |
0.9870769 |
1.232306 |
1 |
-0.1108343 |
| cnvi0111195 |
NC |
0 |
0.02879083 |
2.136721 |
0 |
0.1300069 |
| cnvi0111196 |
NC |
0 |
0.9856321 |
1.333345 |
1 |
0.1193397 |
| cnvi0111197 |
NC |
0 |
0.008793049 |
1.019793 |
0 |
0.1920714 |
| cnvi0111198 |
NC |
0 |
0.9710615 |
1.252683 |
1 |
-0.0502006 |
| cnvi0111199 |
NC |
0 |
0.009417377 |
1.371909 |
0 |
0.1096253 |
| cnvi0111200 |
NC |
0 |
0.9880754 |
0.9076811 |
1 |
0.04145216 |
| cnvi0111201 |
NC |
0 |
0.01948186 |
0.8456966 |
0.001076985 |
-0.1291779 |
| cnvi0111202 |
NC |
0 |
0.9431241 |
1.376075 |
1 |
0.04566851 |
| cnvi0111203 |
NC |
0 |
0.05064996 |
1.936972 |
0.02703292 |
0.2253682 |
| cnvi0111204 |
NC |
0 |
0.9928558 |
1.116234 |
1 |
-0.1263361 |
Total number of rows: 299140
Table truncated, full table size 17190 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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