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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_134 |
| 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) |
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 |
| |
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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 |
0.9761816 |
1.434189 |
1 |
-0.01917896 |
| cnvi0111186 |
NC |
0 |
0.01667443 |
0.578429 |
0 |
0.2159754 |
| cnvi0111187 |
NC |
0 |
0.9818979 |
1.429316 |
0.9966174 |
-0.09629169 |
| cnvi0111188 |
NC |
0 |
0.01875263 |
1.335999 |
0.004172102 |
0.03385482 |
| cnvi0111189 |
NC |
0 |
0.03375152 |
1.533433 |
0.00780159 |
0.08845385 |
| cnvi0111190 |
NC |
0 |
0.00501034 |
0.5276777 |
0 |
0.5565273 |
| cnvi0111191 |
NC |
0 |
0.03560276 |
0.8438323 |
0.00733257 |
-0.381803 |
| cnvi0111192 |
NC |
0 |
0.02638212 |
1.234913 |
0 |
0.1487504 |
| cnvi0111193 |
NC |
0 |
0.002646196 |
1.159797 |
0 |
-0.06595213 |
| cnvi0111194 |
NC |
0 |
0.9895725 |
1.433554 |
1 |
0.107402 |
| cnvi0111195 |
NC |
0 |
0.03506393 |
2.08354 |
0.002660583 |
0.09364551 |
| cnvi0111196 |
NC |
0 |
0.9863364 |
1.159455 |
1 |
-0.08226288 |
| cnvi0111197 |
NC |
0 |
0.01216713 |
0.995179 |
0 |
0.1568228 |
| cnvi0111198 |
NC |
0 |
0.9667933 |
1.317281 |
0.9960709 |
0.02234177 |
| cnvi0111199 |
NC |
0 |
0.009827772 |
1.386055 |
0 |
0.1244254 |
| cnvi0111200 |
NC |
0 |
0.9951843 |
0.7817582 |
1 |
-0.1740108 |
| cnvi0111201 |
NC |
0 |
0.02165147 |
0.7827578 |
0.003344057 |
-0.240752 |
| cnvi0111202 |
NC |
0 |
0.9254443 |
1.308681 |
0.9998024 |
-0.02677752 |
| cnvi0111203 |
NC |
0 |
0.05025942 |
1.925488 |
0.02662212 |
0.2167898 |
| cnvi0111204 |
NC |
0 |
0.9887686 |
1.248283 |
1 |
0.03496882 |
Total number of rows: 299140
Table truncated, full table size 17350 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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