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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_105 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
|
| Label |
C-Bio and A-DNP
|
| 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
|
| Street address |
900 E 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| 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 |
0.9760365 |
1.248378 |
1 |
-0.2193597 |
| cnvi0111186 |
NC |
0 |
0.004610561 |
0.4737636 |
0 |
-0.07199724 |
| cnvi0111187 |
NC |
0 |
0.9836427 |
1.388218 |
0.998434 |
-0.138382 |
| cnvi0111188 |
NC |
0 |
0.01371323 |
1.212176 |
0 |
-0.1064652 |
| cnvi0111189 |
NC |
0 |
0.02862532 |
1.539483 |
0.002401684 |
0.09413453 |
| cnvi0111190 |
NC |
0 |
0.0001659171 |
0.4350698 |
0 |
0.278117 |
| cnvi0111191 |
NC |
0 |
0.02541482 |
0.6784289 |
0 |
-0.6965616 |
| cnvi0111192 |
NC |
0 |
0.01495443 |
1.140229 |
0 |
0.0336638 |
| cnvi0111193 |
NC |
0 |
0.0024177 |
1.159226 |
0 |
-0.06666201 |
| cnvi0111194 |
NC |
0 |
0.9886703 |
1.139877 |
1 |
-0.2233163 |
| cnvi0111195 |
NC |
0 |
0.03055776 |
2.00532 |
0 |
0.03844059 |
| cnvi0111196 |
NC |
0 |
0.9946535 |
0.9809215 |
1 |
-0.3235006 |
| cnvi0111197 |
NC |
0 |
0.004739245 |
1.033885 |
0 |
0.2118704 |
| cnvi0111198 |
NC |
0 |
0.9745788 |
1.262686 |
1 |
-0.03872555 |
| cnvi0111199 |
NC |
0 |
0.007645884 |
1.40449 |
0 |
0.1434875 |
| cnvi0111200 |
NC |
0 |
0.9951486 |
0.959589 |
1 |
0.1216833 |
| cnvi0111201 |
NC |
0 |
0.01646123 |
0.8234497 |
0 |
-0.1676374 |
| cnvi0111202 |
NC |
0 |
0.9326127 |
1.435387 |
1 |
0.1065491 |
| cnvi0111203 |
NC |
0 |
0.04820077 |
1.774202 |
0.02445666 |
0.09873608 |
| cnvi0111204 |
NC |
0 |
0.9911425 |
1.419928 |
1 |
0.2208423 |
Total number of rows: 299140
Table truncated, full table size 17187 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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