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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_49 |
| 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
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| 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 |
0.9761848 |
1.619933 |
1 |
0.1565196 |
| cnvi0111186 |
NC |
0 |
0.01822125 |
0.5307221 |
0 |
0.09179219 |
| cnvi0111187 |
NC |
0 |
0.9833922 |
1.469262 |
0.9981732 |
-0.05652519 |
| cnvi0111188 |
NC |
0 |
0.008037933 |
1.164784 |
0 |
-0.1640021 |
| cnvi0111189 |
NC |
0 |
0.02299413 |
1.463354 |
0 |
0.02096743 |
| cnvi0111190 |
NC |
0 |
0.008195457 |
0.4707302 |
0 |
0.3917708 |
| cnvi0111191 |
NC |
0 |
0.04047789 |
0.4583369 |
0.01248023 |
-1.262351 |
| cnvi0111192 |
NC |
0 |
0.02164703 |
0.9584146 |
0 |
-0.2169374 |
| cnvi0111193 |
NC |
0 |
0.01065918 |
1.010382 |
0 |
-0.2649232 |
| cnvi0111194 |
NC |
0 |
0.9876108 |
1.24177 |
1 |
-0.09979669 |
| cnvi0111195 |
NC |
0 |
0.03448639 |
2.314991 |
0.002048302 |
0.2456151 |
| cnvi0111196 |
NC |
0 |
0.9882184 |
1.047771 |
1 |
-0.2283865 |
| cnvi0111197 |
NC |
0 |
0.01299782 |
0.9310862 |
0.0003090541 |
0.06078145 |
| cnvi0111198 |
NC |
0 |
0.9716217 |
1.250226 |
1 |
-0.05303282 |
| cnvi0111199 |
NC |
0 |
0.006524085 |
1.443531 |
0 |
0.1830423 |
| cnvi0111200 |
NC |
0 |
0.984087 |
0.9229861 |
0.9998949 |
0.06557554 |
| cnvi0111201 |
NC |
0 |
0.02021494 |
0.8712017 |
0.001842991 |
-0.08631127 |
| cnvi0111202 |
NC |
0 |
0.9377808 |
1.14623 |
1 |
-0.2179938 |
| cnvi0111203 |
NC |
0 |
0.03435944 |
1.635363 |
0.00989716 |
-0.018824 |
| cnvi0111204 |
NC |
0 |
0.9856755 |
1.289425 |
0.9971451 |
0.0817527 |
Total number of rows: 299140
Table truncated, full table size 17263 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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