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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_76 |
| Sample type |
genomic |
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| Source name |
Colon tissue, tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| Label |
C-Bio and A-DNP
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| 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
|
| 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 |
0.9855446 |
1.322184 |
1 |
-0.1364913 |
| cnvi0111186 |
NC |
0 |
0.01056642 |
0.5916925 |
0 |
0.2486831 |
| cnvi0111187 |
NC |
0 |
0.9918641 |
1.501187 |
1 |
-0.02551227 |
| cnvi0111188 |
NC |
0 |
0.01009952 |
1.346099 |
0 |
0.04472041 |
| cnvi0111189 |
NC |
0 |
0.02441684 |
1.583401 |
0 |
0.1347154 |
| cnvi0111190 |
NC |
0 |
0.002374136 |
0.4253953 |
0 |
0.2456744 |
| cnvi0111191 |
NC |
0 |
0.04151817 |
0.4268042 |
0.01357866 |
-1.365185 |
| cnvi0111192 |
NC |
0 |
0.01909398 |
1.145219 |
0 |
0.03996444 |
| cnvi0111193 |
NC |
0 |
0.006116672 |
1.134781 |
0 |
-0.09741019 |
| cnvi0111194 |
NC |
0 |
0.9846299 |
1.221372 |
1 |
-0.1236917 |
| cnvi0111195 |
NC |
0 |
0.03139872 |
2.140893 |
0 |
0.1328209 |
| cnvi0111196 |
NC |
0 |
0.9934224 |
1.325802 |
1 |
0.1111552 |
| cnvi0111197 |
NC |
0 |
0.003895692 |
1.012781 |
0 |
0.1821169 |
| cnvi0111198 |
NC |
0 |
0.975577 |
1.364715 |
1 |
0.07337778 |
| cnvi0111199 |
NC |
0 |
0.00842771 |
1.44983 |
0 |
0.1893247 |
| cnvi0111200 |
NC |
0 |
0.9908798 |
0.9094045 |
1 |
0.0441888 |
| cnvi0111201 |
NC |
0 |
0.01533374 |
0.8498972 |
0 |
-0.1220297 |
| cnvi0111202 |
NC |
0 |
0.9476406 |
1.318436 |
1 |
-0.01606331 |
| cnvi0111203 |
NC |
0 |
0.03918407 |
1.968129 |
0.01497212 |
0.2483902 |
| cnvi0111204 |
NC |
0 |
0.9919637 |
1.316003 |
1 |
0.1111874 |
Total number of rows: 299140
Table truncated, full table size 17045 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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