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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_146 |
| 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
|
| 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 |
0.974536 |
1.188318 |
0.9996779 |
-0.2904932 |
| cnvi0111186 |
NC |
0 |
0.02099465 |
0.4491592 |
0 |
-0.1489376 |
| cnvi0111187 |
NC |
0 |
0.9775897 |
1.312459 |
0.9921322 |
-0.2193438 |
| cnvi0111188 |
NC |
0 |
0.01451648 |
1.297551 |
0 |
-0.00827349 |
| cnvi0111189 |
NC |
0 |
0.02627399 |
1.4467 |
0 |
0.004455214 |
| cnvi0111190 |
NC |
0 |
0 |
0.4556422 |
0 |
0.3447717 |
| cnvi0111191 |
NC |
0 |
0.03386106 |
0.5724421 |
0.005493506 |
-0.9416297 |
| cnvi0111192 |
NC |
0 |
0.0263468 |
1.113425 |
0 |
-0.0006552367 |
| cnvi0111193 |
NC |
0 |
0.01056844 |
1.02993 |
0 |
-0.237277 |
| cnvi0111194 |
NC |
0 |
0.9876573 |
1.328328 |
1 |
-0.002583521 |
| cnvi0111195 |
NC |
0 |
0.03590225 |
2.034081 |
0.003549332 |
0.05898536 |
| cnvi0111196 |
NC |
0 |
0.9870961 |
1.055939 |
1 |
-0.2171835 |
| cnvi0111197 |
NC |
0 |
0.009241607 |
1.016244 |
0 |
0.1870423 |
| cnvi0111198 |
NC |
0 |
0.9747432 |
1.20548 |
1 |
-0.1056138 |
| cnvi0111199 |
NC |
0 |
0.01077855 |
1.306754 |
0 |
0.03942799 |
| cnvi0111200 |
NC |
0 |
0.9933054 |
0.8623568 |
1 |
-0.03244849 |
| cnvi0111201 |
NC |
0 |
0.02713931 |
0.770222 |
0.009078415 |
-0.2640437 |
| cnvi0111202 |
NC |
0 |
0.938569 |
1.41902 |
1 |
0.09000424 |
| cnvi0111203 |
NC |
0 |
0.04535447 |
1.770627 |
0.02146267 |
0.09582577 |
| cnvi0111204 |
NC |
0 |
0.9956622 |
1.071224 |
1 |
-0.1857159 |
Total number of rows: 299140
Table truncated, full table size 17399 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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