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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_119 |
| 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 |
0.9792072 |
1.274947 |
1 |
-0.1889771 |
| cnvi0111186 |
NC |
0 |
0.009918922 |
0.5294138 |
0 |
0.0882313 |
| cnvi0111187 |
NC |
0 |
0.9888121 |
1.479595 |
1 |
-0.04641424 |
| cnvi0111188 |
NC |
0 |
0.01518408 |
1.213869 |
0.0004572801 |
-0.1044518 |
| cnvi0111189 |
NC |
0 |
0.02706132 |
1.484916 |
0.0007541714 |
0.04207016 |
| cnvi0111190 |
NC |
0 |
0 |
0.4200626 |
0 |
0.2274745 |
| cnvi0111191 |
NC |
0 |
0.02627243 |
0.8172964 |
0 |
-0.4278999 |
| cnvi0111192 |
NC |
0 |
0.02191093 |
1.155364 |
0 |
0.05268846 |
| cnvi0111193 |
NC |
0 |
0.01057883 |
1.167434 |
0 |
-0.05648327 |
| cnvi0111194 |
NC |
0 |
0.9793347 |
1.132902 |
0.9962775 |
-0.2321713 |
| cnvi0111195 |
NC |
0 |
0.03430734 |
2.091549 |
0.001858476 |
0.09917998 |
| cnvi0111196 |
NC |
0 |
0.9919587 |
1.102518 |
1 |
-0.1549079 |
| cnvi0111197 |
NC |
0 |
0.01081558 |
0.9461399 |
0 |
0.08392022 |
| cnvi0111198 |
NC |
0 |
0.9750322 |
1.107252 |
1 |
-0.2282378 |
| cnvi0111199 |
NC |
0 |
0.009762144 |
1.342343 |
0 |
0.07819401 |
| cnvi0111200 |
NC |
0 |
0.9946194 |
0.7696923 |
1 |
-0.1964515 |
| cnvi0111201 |
NC |
0 |
0.02201985 |
0.7396606 |
0.003728978 |
-0.3224545 |
| cnvi0111202 |
NC |
0 |
0.9449059 |
1.263193 |
1 |
-0.07781538 |
| cnvi0111203 |
NC |
0 |
0.04454115 |
1.777453 |
0.02060716 |
0.1013768 |
| cnvi0111204 |
NC |
0 |
0.9912137 |
1.076606 |
1 |
-0.1784856 |
Total number of rows: 299140
Table truncated, full table size 17279 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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