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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_129 |
| 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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| |
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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 |
0.9840286 |
1.507709 |
1 |
0.05294406 |
| cnvi0111186 |
NC |
0 |
0.01033857 |
0.5331076 |
0 |
0.0982623 |
| cnvi0111187 |
NC |
0 |
0.9862363 |
1.420542 |
1 |
-0.1051749 |
| cnvi0111188 |
NC |
0 |
0.01220163 |
1.292912 |
0 |
-0.01344095 |
| cnvi0111189 |
NC |
0 |
0.02783451 |
1.453729 |
0.00156865 |
0.01144748 |
| cnvi0111190 |
NC |
0 |
0.002698466 |
0.458142 |
0 |
0.3526649 |
| cnvi0111191 |
NC |
0 |
0.02493696 |
1.508296 |
0 |
0.4560888 |
| cnvi0111192 |
NC |
0 |
0.01588263 |
1.080019 |
0 |
-0.04460217 |
| cnvi0111193 |
NC |
0 |
0.006104424 |
1.233458 |
0 |
0.02288456 |
| cnvi0111194 |
NC |
0 |
0.9888066 |
1.269004 |
1 |
-0.06849851 |
| cnvi0111195 |
NC |
0 |
0.02745522 |
2.199257 |
0 |
0.1716249 |
| cnvi0111196 |
NC |
0 |
0.9885086 |
1.294936 |
1 |
0.0771705 |
| cnvi0111197 |
NC |
0 |
0.006370505 |
0.9729792 |
0 |
0.1242758 |
| cnvi0111198 |
NC |
0 |
0.9773575 |
1.271083 |
1 |
-0.02916325 |
| cnvi0111199 |
NC |
0 |
0.006779625 |
1.465188 |
0 |
0.2045263 |
| cnvi0111200 |
NC |
0 |
0.9944146 |
0.9360878 |
1 |
0.08591047 |
| cnvi0111201 |
NC |
0 |
0.01988857 |
0.7941998 |
0.001501961 |
-0.2198161 |
| cnvi0111202 |
NC |
0 |
0.9406922 |
1.361178 |
1 |
0.02996503 |
| cnvi0111203 |
NC |
0 |
0.04566822 |
2.018084 |
0.02179271 |
0.2845514 |
| cnvi0111204 |
NC |
0 |
0.9912984 |
1.259102 |
1 |
0.04741998 |
Total number of rows: 299140
Table truncated, full table size 17143 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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