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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_107 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| 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 |
0.98349 |
1.645514 |
1 |
0.1791238 |
| cnvi0111186 |
NC |
0 |
0.006330138 |
0.5553886 |
0 |
0.1573331 |
| cnvi0111187 |
NC |
0 |
0.9887783 |
1.433478 |
1 |
-0.09209616 |
| cnvi0111188 |
NC |
0 |
0.00567921 |
1.366065 |
0 |
0.06596178 |
| cnvi0111189 |
NC |
0 |
0.02038146 |
1.591376 |
0 |
0.1419636 |
| cnvi0111190 |
NC |
0 |
0.002565387 |
0.2807999 |
0 |
-0.3535872 |
| cnvi0111191 |
NC |
0 |
0.0170183 |
1.603091 |
0 |
0.5440255 |
| cnvi0111192 |
NC |
0 |
0.01275087 |
1.204177 |
0 |
0.1123877 |
| cnvi0111193 |
NC |
0 |
0.004497214 |
1.189733 |
0 |
-0.02918577 |
| cnvi0111194 |
NC |
0 |
0.9916943 |
1.141024 |
1 |
-0.221865 |
| cnvi0111195 |
NC |
0 |
0.02247725 |
2.177824 |
0 |
0.1574959 |
| cnvi0111196 |
NC |
0 |
0.9947045 |
1.146989 |
1 |
-0.09785839 |
| cnvi0111197 |
NC |
0 |
0.004709797 |
1.135098 |
0 |
0.3466111 |
| cnvi0111198 |
NC |
0 |
0.9714277 |
1.08332 |
1 |
-0.2597627 |
| cnvi0111199 |
NC |
0 |
0.00364216 |
1.400974 |
0 |
0.1398712 |
| cnvi0111200 |
NC |
0 |
0.9972217 |
0.919045 |
1 |
0.05940209 |
| cnvi0111201 |
NC |
0 |
0.01748254 |
0.6990632 |
0 |
-0.4038951 |
| cnvi0111202 |
NC |
0 |
0.9431208 |
1.452374 |
1 |
0.1235226 |
| cnvi0111203 |
NC |
0 |
0.03944929 |
1.845331 |
0.0152511 |
0.1554449 |
| cnvi0111204 |
NC |
0 |
0.9938058 |
1.180057 |
1 |
-0.04611969 |
Total number of rows: 299140
Table truncated, full table size 16950 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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