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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_161 |
| 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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| |
|
| 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 |
| |
|
| 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 |
0.9745967 |
1.140605 |
0.9997418 |
-0.3496154 |
| cnvi0111186 |
NC |
0 |
0.01523564 |
0.3762131 |
0 |
-0.4046146 |
| cnvi0111187 |
NC |
0 |
0.9898738 |
1.514745 |
1 |
-0.01254101 |
| cnvi0111188 |
NC |
0 |
0.008592977 |
1.311433 |
0 |
0.007079417 |
| cnvi0111189 |
NC |
0 |
0.02741123 |
1.384975 |
0.001122767 |
-0.05845113 |
| cnvi0111190 |
NC |
0 |
0.001749192 |
0.5024899 |
0 |
0.4859647 |
| cnvi0111191 |
NC |
0 |
0.03118361 |
0.4506377 |
0.002666379 |
-1.286791 |
| cnvi0111192 |
NC |
0 |
0.0195931 |
1.198772 |
0 |
0.1058976 |
| cnvi0111193 |
NC |
0 |
0.001937523 |
1.088905 |
0 |
-0.1569457 |
| cnvi0111194 |
NC |
0 |
0.9897947 |
1.336889 |
1 |
0.006685394 |
| cnvi0111195 |
NC |
0 |
0.03568687 |
2.125987 |
0.003320986 |
0.1227412 |
| cnvi0111196 |
NC |
0 |
0.9919236 |
1.258214 |
1 |
0.03566654 |
| cnvi0111197 |
NC |
0 |
0.0130427 |
0.8926166 |
0.0003556822 |
-9.267249E-05 |
| cnvi0111198 |
NC |
0 |
0.9673136 |
1.305789 |
0.9966208 |
0.009699759 |
| cnvi0111199 |
NC |
0 |
0.012468 |
1.348473 |
0 |
0.08476765 |
| cnvi0111200 |
NC |
0 |
0.986842 |
0.8664685 |
1 |
-0.02558608 |
| cnvi0111201 |
NC |
0 |
0.01616625 |
0.8264568 |
0 |
-0.1623785 |
| cnvi0111202 |
NC |
0 |
0.9372326 |
1.394037 |
1 |
0.06437811 |
| cnvi0111203 |
NC |
0 |
0.03284219 |
1.936791 |
0.008301177 |
0.2252337 |
| cnvi0111204 |
NC |
0 |
0.9910863 |
1.287678 |
1 |
0.07979604 |
Total number of rows: 299140
Table truncated, full table size 17222 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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