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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_127 |
| 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.
|
| 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) |
[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 |
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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 |
0.9776505 |
1.350102 |
1 |
-0.1063461 |
| cnvi0111186 |
NC |
0 |
0.00686779 |
0.564796 |
0 |
0.1815652 |
| cnvi0111187 |
NC |
0 |
0.9835901 |
1.490688 |
0.9983792 |
-0.03563822 |
| cnvi0111188 |
NC |
0 |
0.008968352 |
1.235149 |
0 |
-0.07937967 |
| cnvi0111189 |
NC |
0 |
0.01795965 |
1.409908 |
0 |
-0.0327103 |
| cnvi0111190 |
NC |
0 |
0 |
0.5819297 |
0 |
0.697715 |
| cnvi0111191 |
NC |
0 |
0.02338522 |
1.176049 |
0 |
0.0971172 |
| cnvi0111192 |
NC |
0 |
0.01842185 |
1.060989 |
0 |
-0.07024977 |
| cnvi0111193 |
NC |
0 |
0.006578161 |
1.187728 |
0 |
-0.03161896 |
| cnvi0111194 |
NC |
0 |
0.9866632 |
1.155402 |
1 |
-0.2038 |
| cnvi0111195 |
NC |
0 |
0.03398328 |
1.876402 |
0.001514927 |
-0.05742254 |
| cnvi0111196 |
NC |
0 |
0.9866059 |
1.16683 |
1 |
-0.07311592 |
| cnvi0111197 |
NC |
0 |
0.006904372 |
1.031382 |
0 |
0.2083742 |
| cnvi0111198 |
NC |
0 |
0.9740503 |
1.190321 |
1 |
-0.123871 |
| cnvi0111199 |
NC |
0 |
0.01013956 |
1.411511 |
0 |
0.1506814 |
| cnvi0111200 |
NC |
0 |
0.9942065 |
0.8048354 |
1 |
-0.1320395 |
| cnvi0111201 |
NC |
0 |
0.01856992 |
0.748947 |
0.0001240777 |
-0.3044545 |
| cnvi0111202 |
NC |
0 |
0.9339902 |
1.329992 |
1 |
-0.003472731 |
| cnvi0111203 |
NC |
0 |
0.03870073 |
1.856886 |
0.01446369 |
0.1644508 |
| cnvi0111204 |
NC |
0 |
0.9891485 |
1.336152 |
1 |
0.1331081 |
Total number of rows: 299140
Table truncated, full table size 17131 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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