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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_145 |
| 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) |
kibriya@uchicago.edu
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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 |
0.9771554 |
1.37496 |
1 |
-0.08002485 |
| cnvi0111186 |
NC |
0 |
0.0137943 |
0.4878853 |
0 |
-0.02962246 |
| cnvi0111187 |
NC |
0 |
0.9830621 |
1.457731 |
0.9978296 |
-0.06789223 |
| cnvi0111188 |
NC |
0 |
0.01132126 |
1.45616 |
0 |
0.1581041 |
| cnvi0111189 |
NC |
0 |
0.0293374 |
1.627729 |
0.003151782 |
0.1745492 |
| cnvi0111190 |
NC |
0 |
0.001047791 |
0.4998383 |
0 |
0.4783317 |
| cnvi0111191 |
NC |
0 |
0.03166968 |
1.284626 |
0.003179625 |
0.2245173 |
| cnvi0111192 |
NC |
0 |
0.02400824 |
1.151612 |
0 |
0.0479959 |
| cnvi0111193 |
NC |
0 |
0.01012444 |
1.170934 |
0 |
-0.05216422 |
| cnvi0111194 |
NC |
0 |
0.9870183 |
1.189842 |
1 |
-0.1614244 |
| cnvi0111195 |
NC |
0 |
0.02940175 |
1.989335 |
0 |
0.02689469 |
| cnvi0111196 |
NC |
0 |
0.9867581 |
1.344742 |
1 |
0.1316195 |
| cnvi0111197 |
NC |
0 |
0.009388455 |
1.080848 |
0 |
0.2759582 |
| cnvi0111198 |
NC |
0 |
0.9664379 |
1.225439 |
0.9956954 |
-0.081923 |
| cnvi0111199 |
NC |
0 |
0.01223545 |
1.436577 |
0 |
0.1760758 |
| cnvi0111200 |
NC |
0 |
0.9911146 |
0.8855809 |
1 |
0.005890735 |
| cnvi0111201 |
NC |
0 |
0.02533047 |
0.7549974 |
0.007188323 |
-0.2928463 |
| cnvi0111202 |
NC |
0 |
0.9435518 |
1.376318 |
1 |
0.0459232 |
| cnvi0111203 |
NC |
0 |
0.04330825 |
1.884622 |
0.01931029 |
0.1858409 |
| cnvi0111204 |
NC |
0 |
0.9941873 |
1.160366 |
1 |
-0.07039556 |
Total number of rows: 299140
Table truncated, full table size 17116 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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