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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_135 |
| 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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| Label |
C-Bio and A-DNP
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| Label protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.
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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
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| Department |
Health Studies
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| 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 |
0.9803209 |
1.364289 |
1 |
-0.09126511 |
| cnvi0111186 |
NC |
0 |
0.00768424 |
0.5665627 |
0 |
0.1860711 |
| cnvi0111187 |
NC |
0 |
0.9887185 |
1.438083 |
1 |
-0.08746976 |
| cnvi0111188 |
NC |
0 |
0.01211492 |
1.554143 |
0 |
0.252055 |
| cnvi0111189 |
NC |
0 |
0.02225806 |
1.555273 |
0 |
0.1088568 |
| cnvi0111190 |
NC |
0 |
0 |
0.4304641 |
0 |
0.262763 |
| cnvi0111191 |
NC |
0 |
0.02154893 |
1.309246 |
0 |
0.2519051 |
| cnvi0111192 |
NC |
0 |
0.01332671 |
1.13456 |
0 |
0.02647372 |
| cnvi0111193 |
NC |
0 |
0.004354467 |
1.109161 |
0 |
-0.1303547 |
| cnvi0111194 |
NC |
0 |
0.9893689 |
1.379728 |
1 |
0.05218876 |
| cnvi0111195 |
NC |
0 |
0.02682775 |
2.182198 |
0 |
0.1603905 |
| cnvi0111196 |
NC |
0 |
0.9900967 |
1.284719 |
1 |
0.06574219 |
| cnvi0111197 |
NC |
0 |
0.003310172 |
1.034585 |
0 |
0.2128468 |
| cnvi0111198 |
NC |
0 |
0.9708106 |
1.216662 |
1 |
-0.09229355 |
| cnvi0111199 |
NC |
0 |
0.007276952 |
1.461969 |
0 |
0.2013539 |
| cnvi0111200 |
NC |
0 |
0.9911115 |
0.9333869 |
1 |
0.08174179 |
| cnvi0111201 |
NC |
0 |
0.01593207 |
0.8061509 |
0 |
-0.1982682 |
| cnvi0111202 |
NC |
0 |
0.9367167 |
1.336047 |
1 |
0.003079684 |
| cnvi0111203 |
NC |
0 |
0.04536832 |
2.00218 |
0.02147725 |
0.273137 |
| cnvi0111204 |
NC |
0 |
0.9867975 |
1.191315 |
0.9983094 |
-0.03242071 |
Total number of rows: 299140
Table truncated, full table size 17041 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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