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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_141 |
| 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
|
| 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 |
0.9842408 |
1.173802 |
1 |
-0.3082251 |
| cnvi0111186 |
NC |
0 |
0.01108844 |
0.5412467 |
0 |
0.1201216 |
| cnvi0111187 |
NC |
0 |
0.9852312 |
1.399161 |
1 |
-0.1270541 |
| cnvi0111188 |
NC |
0 |
0.01145685 |
1.364604 |
0 |
0.06441784 |
| cnvi0111189 |
NC |
0 |
0.02804688 |
1.526102 |
0.00179236 |
0.08154077 |
| cnvi0111190 |
NC |
0 |
0.008990296 |
0.4951986 |
0 |
0.4648774 |
| cnvi0111191 |
NC |
0 |
0.02702356 |
1.015198 |
0 |
-0.1150696 |
| cnvi0111192 |
NC |
0 |
0.01660097 |
1.004132 |
0 |
-0.1497097 |
| cnvi0111193 |
NC |
0 |
0.003481009 |
1.070627 |
0 |
-0.181368 |
| cnvi0111194 |
NC |
0 |
0.9885962 |
1.215619 |
1 |
-0.130504 |
| cnvi0111195 |
NC |
0 |
0.0294442 |
1.997438 |
0 |
0.03275901 |
| cnvi0111196 |
NC |
0 |
0.9859827 |
1.262686 |
1 |
0.04078598 |
| cnvi0111197 |
NC |
0 |
0.006706183 |
0.9600784 |
0 |
0.105019 |
| cnvi0111198 |
NC |
0 |
0.9685881 |
1.170501 |
0.9979676 |
-0.1480957 |
| cnvi0111199 |
NC |
0 |
0.003279638 |
1.431803 |
0 |
0.1712742 |
| cnvi0111200 |
NC |
0 |
0.9931172 |
0.827476 |
1 |
-0.09201586 |
| cnvi0111201 |
NC |
0 |
0.02489905 |
0.7140331 |
0.006737517 |
-0.373327 |
| cnvi0111202 |
NC |
0 |
0.9384854 |
1.391666 |
1 |
0.06192182 |
| cnvi0111203 |
NC |
0 |
0.04483243 |
1.764913 |
0.02091355 |
0.09116256 |
| cnvi0111204 |
NC |
0 |
0.9947484 |
1.183805 |
1 |
-0.04154398 |
Total number of rows: 299140
Table truncated, full table size 17176 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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