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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_153 |
| 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 |
0.9784227 |
1.287142 |
1 |
-0.1752427 |
| cnvi0111186 |
NC |
0 |
0.01304921 |
0.4441618 |
0 |
-0.1650791 |
| cnvi0111187 |
NC |
0 |
0.9843386 |
1.523728 |
0.9991585 |
-0.004010773 |
| cnvi0111188 |
NC |
0 |
0.006875705 |
1.251341 |
0 |
-0.06058912 |
| cnvi0111189 |
NC |
0 |
0.02428792 |
1.544846 |
0 |
0.09915239 |
| cnvi0111190 |
NC |
0 |
0.003711485 |
0.4612423 |
0 |
0.3623949 |
| cnvi0111191 |
NC |
0 |
0.03652202 |
0.7995111 |
0.008303214 |
-0.4596413 |
| cnvi0111192 |
NC |
0 |
0.02220864 |
1.112963 |
0 |
-0.001253904 |
| cnvi0111193 |
NC |
0 |
0.007947064 |
1.034504 |
0 |
-0.2308851 |
| cnvi0111194 |
NC |
0 |
0.9899947 |
1.226073 |
1 |
-0.1181498 |
| cnvi0111195 |
NC |
0 |
0.03630544 |
2.220527 |
0.003976769 |
0.1855105 |
| cnvi0111196 |
NC |
0 |
0.9911533 |
1.109129 |
1 |
-0.1462836 |
| cnvi0111197 |
NC |
0 |
0.008805132 |
1.033273 |
0 |
0.2110161 |
| cnvi0111198 |
NC |
0 |
0.973129 |
1.285363 |
1 |
-0.01304623 |
| cnvi0111199 |
NC |
0 |
0.006100345 |
1.451049 |
0 |
0.190537 |
| cnvi0111200 |
NC |
0 |
0.9870154 |
0.8626684 |
1 |
-0.03192727 |
| cnvi0111201 |
NC |
0 |
0.02564789 |
0.8495291 |
0.007519993 |
-0.1226546 |
| cnvi0111202 |
NC |
0 |
0.9403914 |
1.418263 |
1 |
0.08923417 |
| cnvi0111203 |
NC |
0 |
0.04740303 |
1.941194 |
0.02361752 |
0.2285095 |
| cnvi0111204 |
NC |
0 |
0.9892889 |
1.319163 |
1 |
0.1146467 |
Total number of rows: 299140
Table truncated, full table size 17206 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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