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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_126 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, normal
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: normal colon mucosa
|
| 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) |
[email protected]
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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 |
0.9832193 |
1.280358 |
1 |
-0.1828667 |
| cnvi0111186 |
NC |
0 |
0.0003475471 |
0.5103571 |
0 |
0.03534246 |
| cnvi0111187 |
NC |
0 |
0.9922213 |
1.375958 |
1 |
-0.1511798 |
| cnvi0111188 |
NC |
0 |
0.007304278 |
1.22466 |
0 |
-0.09168305 |
| cnvi0111189 |
NC |
0 |
0.02368989 |
1.516449 |
0 |
0.07238571 |
| cnvi0111190 |
NC |
0 |
0 |
0.4544978 |
0 |
0.3411435 |
| cnvi0111191 |
NC |
0 |
0.02235341 |
0.8810258 |
0 |
-0.3195751 |
| cnvi0111192 |
NC |
0 |
0.01193775 |
1.158788 |
0 |
0.05695743 |
| cnvi0111193 |
NC |
0 |
0.00160174 |
1.105303 |
0 |
-0.1353823 |
| cnvi0111194 |
NC |
0 |
0.9915982 |
1.203068 |
1 |
-0.1454759 |
| cnvi0111195 |
NC |
0 |
0.03139419 |
2.03788 |
0 |
0.06167781 |
| cnvi0111196 |
NC |
0 |
0.9953318 |
1.036848 |
1 |
-0.2435056 |
| cnvi0111197 |
NC |
0 |
0.001148257 |
0.944916 |
0 |
0.08205274 |
| cnvi0111198 |
NC |
0 |
0.9718448 |
1.182997 |
1 |
-0.1327754 |
| cnvi0111199 |
NC |
0 |
0.009568099 |
1.467577 |
0 |
0.2068765 |
| cnvi0111200 |
NC |
0 |
0.9967987 |
0.9348239 |
1 |
0.0839613 |
| cnvi0111201 |
NC |
0 |
0.01235053 |
0.7920141 |
0 |
-0.2237919 |
| cnvi0111202 |
NC |
0 |
0.9377805 |
1.368849 |
1 |
0.03807298 |
| cnvi0111203 |
NC |
0 |
0.04345921 |
1.902114 |
0.01946908 |
0.1991691 |
| cnvi0111204 |
NC |
0 |
0.9909188 |
1.262318 |
1 |
0.05110025 |
Total number of rows: 299140
Table truncated, full table size 17049 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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