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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_148 |
| Sample type |
genomic |
| |
|
| 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
|
| 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 |
0.9553581 |
1.422757 |
0.9795007 |
-0.03072477 |
| cnvi0111186 |
NC |
0 |
0.1032097 |
0.1156178 |
0.07731386 |
-2.106801 |
| cnvi0111187 |
NC |
0 |
0.9940131 |
2.069295 |
1 |
0.437523 |
| cnvi0111188 |
NC |
0 |
0.01981949 |
0.5769816 |
0.005282696 |
-1.177467 |
| cnvi0111189 |
NC |
0 |
0.04536657 |
0.8837221 |
0.0200368 |
-0.7066464 |
| cnvi0111190 |
NC |
0 |
0.0005200345 |
0.8690241 |
0 |
1.276266 |
| cnvi0111191 |
NC |
0 |
0.08521485 |
0.5185835 |
0.05971804 |
-1.084183 |
| cnvi0111192 |
NC |
0 |
0.0202374 |
3.345968 |
0 |
1.586765 |
| cnvi0111193 |
NC |
0 |
0 |
0.8263611 |
0 |
-0.5549797 |
| cnvi0111194 |
NC |
0 |
0.9877647 |
2.667376 |
1 |
1.003227 |
| cnvi0111195 |
NC |
0 |
0.04609237 |
1.621947 |
0.01435242 |
-0.2676653 |
| cnvi0111196 |
NC |
0 |
0.9712954 |
0.8909261 |
0.9874293 |
-0.4623325 |
| cnvi0111197 |
NC |
0 |
0.0126847 |
0.8601494 |
0 |
-0.05354602 |
| cnvi0111198 |
NC |
0 |
0.9571443 |
1.628955 |
0.9858738 |
0.328725 |
| cnvi0111199 |
NC |
0 |
0.02721234 |
2.619816 |
0.01018472 |
1.042906 |
| cnvi0111200 |
NC |
0 |
0.9841452 |
1.005788 |
0.9999555 |
0.1895208 |
| cnvi0111201 |
NC |
0 |
0.06701564 |
0.6104802 |
0.05074603 |
-0.5993735 |
| cnvi0111202 |
NC |
0 |
0.9551358 |
2.235574 |
1 |
0.7457542 |
| cnvi0111203 |
NC |
0 |
0.02704834 |
1.439093 |
0.002206708 |
-0.2032746 |
| cnvi0111204 |
NC |
0 |
0.9939134 |
1.367082 |
1 |
0.1661246 |
Total number of rows: 299140
Table truncated, full table size 17864 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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