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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_108 |
| 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
|
| Street address |
900 E 57th Street
|
| 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 |
0.9824433 |
1.617342 |
1 |
0.1542108 |
| cnvi0111186 |
NC |
0 |
0.01085868 |
0.5372093 |
0 |
0.1093197 |
| cnvi0111187 |
NC |
0 |
0.9850187 |
1.526533 |
0.9998666 |
-0.001357505 |
| cnvi0111188 |
NC |
0 |
0.009713903 |
1.348858 |
0 |
0.04767346 |
| cnvi0111189 |
NC |
0 |
0.02370768 |
1.52645 |
0 |
0.08186913 |
| cnvi0111190 |
NC |
0 |
0.003615362 |
0.4471121 |
0 |
0.3175068 |
| cnvi0111191 |
NC |
0 |
0.02421203 |
1.423855 |
0 |
0.3729708 |
| cnvi0111192 |
NC |
0 |
0.017455 |
1.174313 |
0 |
0.07615747 |
| cnvi0111193 |
NC |
0 |
0.003510387 |
1.17422 |
0 |
-0.04812139 |
| cnvi0111194 |
NC |
0 |
0.9875047 |
1.354764 |
1 |
0.02584658 |
| cnvi0111195 |
NC |
0 |
0.03027407 |
2.090907 |
0 |
0.09873737 |
| cnvi0111196 |
NC |
0 |
0.9848781 |
1.082116 |
1 |
-0.1818547 |
| cnvi0111197 |
NC |
0 |
0.007915413 |
0.9888303 |
0 |
0.1475896 |
| cnvi0111198 |
NC |
0 |
0.9667904 |
1.163771 |
0.9960678 |
-0.1564151 |
| cnvi0111199 |
NC |
0 |
0.007934393 |
1.429654 |
0 |
0.1691067 |
| cnvi0111200 |
NC |
0 |
0.992507 |
0.8539175 |
1 |
-0.04663661 |
| cnvi0111201 |
NC |
0 |
0.01786103 |
0.7919306 |
0 |
-0.223944 |
| cnvi0111202 |
NC |
0 |
0.9318331 |
1.48427 |
1 |
0.1548626 |
| cnvi0111203 |
NC |
0 |
0.04839997 |
1.949868 |
0.0246662 |
0.2349416 |
| cnvi0111204 |
NC |
0 |
0.991448 |
1.190048 |
1 |
-0.03395655 |
Total number of rows: 299140
Table truncated, full table size 17095 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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