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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_75 |
| 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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| 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
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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 |
0.976945 |
1.33933 |
1 |
-0.1179025 |
| cnvi0111186 |
NC |
0 |
0.02278065 |
0.3831316 |
0 |
-0.3783246 |
| cnvi0111187 |
NC |
0 |
0.987411 |
1.610052 |
1 |
0.07549066 |
| cnvi0111188 |
NC |
0 |
0.01712658 |
1.298007 |
0.002479397 |
-0.007766465 |
| cnvi0111189 |
NC |
0 |
0.02806149 |
1.417564 |
0.001807745 |
-0.02489687 |
| cnvi0111190 |
NC |
0 |
0.01105873 |
0.4244654 |
0 |
0.2425172 |
| cnvi0111191 |
NC |
0 |
0.03467686 |
0.7551535 |
0.006354912 |
-0.5419893 |
| cnvi0111192 |
NC |
0 |
0.02565653 |
1.252115 |
0 |
0.1687085 |
| cnvi0111193 |
NC |
0 |
0.006847725 |
0.9443919 |
0 |
-0.3623663 |
| cnvi0111194 |
NC |
0 |
0.9827467 |
1.311766 |
0.9998379 |
-0.02068481 |
| cnvi0111195 |
NC |
0 |
0.03329048 |
2.009494 |
0.0007804449 |
0.04144055 |
| cnvi0111196 |
NC |
0 |
0.9888099 |
1.082973 |
1 |
-0.1807128 |
| cnvi0111197 |
NC |
0 |
0.01076449 |
1.004305 |
0 |
0.1699925 |
| cnvi0111198 |
NC |
0 |
0.9674667 |
1.216679 |
0.9967826 |
-0.09227376 |
| cnvi0111199 |
NC |
0 |
0.01497948 |
1.602805 |
0 |
0.3340394 |
| cnvi0111200 |
NC |
0 |
0.9893314 |
0.8720815 |
1 |
-0.01627047 |
| cnvi0111201 |
NC |
0 |
0.0224706 |
0.7373869 |
0.004199985 |
-0.3268962 |
| cnvi0111202 |
NC |
0 |
0.9334309 |
1.393004 |
1 |
0.06330909 |
| cnvi0111203 |
NC |
0 |
0.03725414 |
1.982196 |
0.01294205 |
0.2586648 |
| cnvi0111204 |
NC |
0 |
0.9932517 |
1.256073 |
1 |
0.04394419 |
Total number of rows: 299140
Table truncated, full table size 17418 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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