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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_51 |
| 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.
|
| 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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| |
|
| 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
|
| Department |
Health Studies
|
| Street address |
900 E 57th Street
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| 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 |
0.9701748 |
1.458451 |
0.9950895 |
0.005023107 |
| cnvi0111186 |
NC |
0 |
0.02297303 |
0.3542337 |
0 |
-0.4914629 |
| cnvi0111187 |
NC |
0 |
0.9874019 |
1.741432 |
1 |
0.1886578 |
| cnvi0111188 |
NC |
0 |
0.01156006 |
1.051783 |
0 |
-0.3112275 |
| cnvi0111189 |
NC |
0 |
0.02779034 |
1.394974 |
0.001522123 |
-0.04807255 |
| cnvi0111190 |
NC |
0 |
0.004477569 |
0.6009459 |
0 |
0.7441053 |
| cnvi0111191 |
NC |
0 |
0.07104348 |
0.2323421 |
0.04475448 |
-2.242509 |
| cnvi0111192 |
NC |
0 |
0.01499854 |
1.38337 |
0 |
0.3125278 |
| cnvi0111193 |
NC |
0 |
0.006289277 |
1.340286 |
0 |
0.1427173 |
| cnvi0111194 |
NC |
0 |
0.9843318 |
1.696837 |
1 |
0.3506536 |
| cnvi0111195 |
NC |
0 |
0.03465844 |
2.769721 |
0.002230693 |
0.5043489 |
| cnvi0111196 |
NC |
0 |
0.9859713 |
1.110911 |
1 |
-0.1439676 |
| cnvi0111197 |
NC |
0 |
0.02129656 |
0.906646 |
0.00893007 |
0.02240612 |
| cnvi0111198 |
NC |
0 |
0.9795026 |
1.414608 |
1 |
0.1251807 |
| cnvi0111199 |
NC |
0 |
0.01028337 |
1.955263 |
0 |
0.6208037 |
| cnvi0111200 |
NC |
0 |
0.9908711 |
1.114245 |
1 |
0.3372618 |
| cnvi0111201 |
NC |
0 |
0.02354877 |
0.7332521 |
0.005326582 |
-0.3350087 |
| cnvi0111202 |
NC |
0 |
0.9400031 |
1.524834 |
1 |
0.1937618 |
| cnvi0111203 |
NC |
0 |
0.02784726 |
1.99237 |
0.003047087 |
0.2660514 |
| cnvi0111204 |
NC |
0 |
0.9858803 |
1.57865 |
0.9973575 |
0.3737152 |
Total number of rows: 299140
Table truncated, full table size 17347 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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