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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_164 |
| 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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| |
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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) |
[email protected]
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| Organization name |
The University of Chicago
|
| Department |
Health Studies
|
| 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 |
0.9766706 |
1.387233 |
1 |
-0.06720368 |
| cnvi0111186 |
NC |
0 |
0.01066354 |
0.5710695 |
0 |
0.1975017 |
| cnvi0111187 |
NC |
0 |
0.98932 |
1.467266 |
1 |
-0.05848635 |
| cnvi0111188 |
NC |
0 |
0.01016896 |
1.336956 |
0 |
0.03488699 |
| cnvi0111189 |
NC |
0 |
0.02176963 |
1.464906 |
0 |
0.02249717 |
| cnvi0111190 |
NC |
0 |
0 |
0.4328883 |
0 |
0.2708651 |
| cnvi0111191 |
NC |
0 |
0.0275461 |
1.203806 |
0 |
0.1307718 |
| cnvi0111192 |
NC |
0 |
0.0128649 |
1.076476 |
0 |
-0.04934273 |
| cnvi0111193 |
NC |
0 |
0.008765354 |
1.207709 |
0 |
-0.007551115 |
| cnvi0111194 |
NC |
0 |
0.9906842 |
1.292155 |
1 |
-0.04241527 |
| cnvi0111195 |
NC |
0 |
0.03211493 |
2.413835 |
0 |
0.3059357 |
| cnvi0111196 |
NC |
0 |
0.9954985 |
1.129532 |
1 |
-0.1199853 |
| cnvi0111197 |
NC |
0 |
0.01046932 |
0.975412 |
0 |
0.1278784 |
| cnvi0111198 |
NC |
0 |
0.978783 |
1.370677 |
1 |
0.07966674 |
| cnvi0111199 |
NC |
0 |
0.006801361 |
1.502802 |
0 |
0.2410956 |
| cnvi0111200 |
NC |
0 |
0.997259 |
0.8625776 |
1 |
-0.03207909 |
| cnvi0111201 |
NC |
0 |
0.02728063 |
0.8648034 |
0.009226087 |
-0.09694587 |
| cnvi0111202 |
NC |
0 |
0.9394345 |
1.40406 |
1 |
0.07471434 |
| cnvi0111203 |
NC |
0 |
0.032401 |
1.876118 |
0.007837104 |
0.1793161 |
| cnvi0111204 |
NC |
0 |
0.9856373 |
1.315284 |
0.9971055 |
0.110399 |
Total number of rows: 299140
Table truncated, full table size 17158 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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