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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_125 |
| 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.
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| 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
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| 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 |
0.9761928 |
1.351112 |
1 |
-0.105267 |
| cnvi0111186 |
NC |
0 |
0.01010905 |
0.5196025 |
0 |
0.06124393 |
| cnvi0111187 |
NC |
0 |
0.983885 |
1.367176 |
0.9986863 |
-0.1604178 |
| cnvi0111188 |
NC |
0 |
0.01003302 |
1.230456 |
0 |
-0.08487158 |
| cnvi0111189 |
NC |
0 |
0.02226632 |
1.476033 |
0 |
0.03341369 |
| cnvi0111190 |
NC |
0 |
0 |
0.5677843 |
0 |
0.6622132 |
| cnvi0111191 |
NC |
0 |
0.02186239 |
0.8940172 |
0 |
-0.2984568 |
| cnvi0111192 |
NC |
0 |
0.0166944 |
1.170216 |
0 |
0.07111519 |
| cnvi0111193 |
NC |
0 |
0.01062999 |
1.213913 |
0 |
-0.0001586687 |
| cnvi0111194 |
NC |
0 |
0.992631 |
1.513843 |
1 |
0.1860205 |
| cnvi0111195 |
NC |
0 |
0.03376032 |
1.977795 |
0.001278557 |
0.01850131 |
| cnvi0111196 |
NC |
0 |
0.9910345 |
1.188095 |
1 |
-0.04705948 |
| cnvi0111197 |
NC |
0 |
0.006844569 |
1.089429 |
0 |
0.2873669 |
| cnvi0111198 |
NC |
0 |
0.9719658 |
1.344502 |
1 |
0.05184972 |
| cnvi0111199 |
NC |
0 |
0.01224074 |
1.294471 |
0 |
0.02580349 |
| cnvi0111200 |
NC |
0 |
0.9878989 |
0.7699413 |
1 |
-0.195985 |
| cnvi0111201 |
NC |
0 |
0.01570328 |
0.8177083 |
0 |
-0.1777317 |
| cnvi0111202 |
NC |
0 |
0.9387422 |
1.510708 |
1 |
0.1803339 |
| cnvi0111203 |
NC |
0 |
0.04558784 |
1.789819 |
0.02170816 |
0.1113787 |
| cnvi0111204 |
NC |
0 |
0.9924686 |
1.121916 |
1 |
-0.1190113 |
Total number of rows: 299140
Table truncated, full table size 17194 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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