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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_110 |
| 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
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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
|
| 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 |
0.9811864 |
1.443325 |
1 |
-0.01001844 |
| cnvi0111186 |
NC |
0 |
0.01295069 |
0.470534 |
0 |
-0.08186559 |
| cnvi0111187 |
NC |
0 |
0.9812263 |
1.487333 |
0.9959182 |
-0.03888831 |
| cnvi0111188 |
NC |
0 |
0.008675544 |
1.594331 |
0 |
0.2888862 |
| cnvi0111189 |
NC |
0 |
0.01755469 |
1.547685 |
0 |
0.1018004 |
| cnvi0111190 |
NC |
0 |
0 |
0.4100741 |
0 |
0.1927548 |
| cnvi0111191 |
NC |
0 |
0.02250532 |
1.169293 |
0 |
0.08880543 |
| cnvi0111192 |
NC |
0 |
0.01587249 |
1.377475 |
0 |
0.306367 |
| cnvi0111193 |
NC |
0 |
0.007538181 |
1.248963 |
0 |
0.04090666 |
| cnvi0111194 |
NC |
0 |
0.9900445 |
1.33421 |
1 |
0.003791093 |
| cnvi0111195 |
NC |
0 |
0.02573816 |
2.387916 |
0 |
0.2903607 |
| cnvi0111196 |
NC |
0 |
0.9854459 |
1.174623 |
1 |
-0.06351301 |
| cnvi0111197 |
NC |
0 |
0.002375055 |
1.131402 |
0 |
0.3419066 |
| cnvi0111198 |
NC |
0 |
0.9841515 |
1.415699 |
1 |
0.1262928 |
| cnvi0111199 |
NC |
0 |
0.005535424 |
1.577656 |
0 |
0.3112234 |
| cnvi0111200 |
NC |
0 |
0.9924322 |
0.9044428 |
1 |
0.03629588 |
| cnvi0111201 |
NC |
0 |
0.01443054 |
0.8097031 |
0 |
-0.191925 |
| cnvi0111202 |
NC |
0 |
0.9366198 |
1.507519 |
1 |
0.1772851 |
| cnvi0111203 |
NC |
0 |
0.04556699 |
2.557683 |
0.02168623 |
0.6264029 |
| cnvi0111204 |
NC |
0 |
0.9920616 |
1.288169 |
1 |
0.08034633 |
Total number of rows: 299140
Table truncated, full table size 16899 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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