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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_55 |
| 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) |
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 |
0.9740506 |
1.368846 |
0.9991672 |
-0.08645449 |
| cnvi0111186 |
NC |
0 |
0.009337671 |
0.5839319 |
0 |
0.2296356 |
| cnvi0111187 |
NC |
0 |
0.9815475 |
1.475674 |
0.9962527 |
-0.05024268 |
| cnvi0111188 |
NC |
0 |
0.009172992 |
1.359336 |
0 |
0.05883799 |
| cnvi0111189 |
NC |
0 |
0.02599462 |
1.509008 |
0 |
0.06528914 |
| cnvi0111190 |
NC |
0 |
0.0008276 |
0.4794373 |
0 |
0.4182124 |
| cnvi0111191 |
NC |
0 |
0.02961983 |
0.9156404 |
0.001015178 |
-0.2639782 |
| cnvi0111192 |
NC |
0 |
0.0223943 |
1.101405 |
0 |
-0.01631439 |
| cnvi0111193 |
NC |
0 |
0.007749205 |
1.297829 |
0 |
0.09627587 |
| cnvi0111194 |
NC |
0 |
0.9859158 |
1.242043 |
1 |
-0.09947901 |
| cnvi0111195 |
NC |
0 |
0.03092365 |
2.328609 |
0 |
0.2540767 |
| cnvi0111196 |
NC |
0 |
0.9864027 |
1.135272 |
1 |
-0.1126717 |
| cnvi0111197 |
NC |
0 |
0.01183532 |
0.9384992 |
0 |
0.07222218 |
| cnvi0111198 |
NC |
0 |
0.9673632 |
1.307278 |
0.9966732 |
0.01134398 |
| cnvi0111199 |
NC |
0 |
0.01019087 |
1.443323 |
0 |
0.1828349 |
| cnvi0111200 |
NC |
0 |
0.9932234 |
0.8807496 |
1 |
-0.00200148 |
| cnvi0111201 |
NC |
0 |
0.02847508 |
0.8390157 |
0.01047419 |
-0.1406203 |
| cnvi0111202 |
NC |
0 |
0.9397952 |
1.387563 |
1 |
0.05766215 |
| cnvi0111203 |
NC |
0 |
0.0327894 |
1.874306 |
0.008245654 |
0.1779221 |
| cnvi0111204 |
NC |
0 |
0.9914801 |
1.304392 |
1 |
0.09840137 |
Total number of rows: 299140
Table truncated, full table size 17249 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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