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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_70 |
| 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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| 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 |
0.9789692 |
1.282632 |
1 |
-0.1803064 |
| cnvi0111186 |
NC |
0 |
0.0116131 |
0.5834318 |
0 |
0.2283996 |
| cnvi0111187 |
NC |
0 |
0.9874219 |
1.638086 |
1 |
0.100395 |
| cnvi0111188 |
NC |
0 |
0.007210484 |
1.226565 |
0 |
-0.0894411 |
| cnvi0111189 |
NC |
0 |
0.02572744 |
1.566269 |
0 |
0.1190209 |
| cnvi0111190 |
NC |
0 |
0 |
0.551905 |
0 |
0.6212901 |
| cnvi0111191 |
NC |
0 |
0.02534357 |
0.9687315 |
0 |
-0.1826625 |
| cnvi0111192 |
NC |
0 |
0.01765831 |
1.171429 |
0 |
0.07261053 |
| cnvi0111193 |
NC |
0 |
0.005997356 |
1.078637 |
0 |
-0.1706147 |
| cnvi0111194 |
NC |
0 |
0.9896342 |
1.273917 |
1 |
-0.06292374 |
| cnvi0111195 |
NC |
0 |
0.03028429 |
1.970785 |
0 |
0.01337856 |
| cnvi0111196 |
NC |
0 |
0.9917539 |
1.205402 |
1 |
-0.02619627 |
| cnvi0111197 |
NC |
0 |
0.005418971 |
1.040707 |
0 |
0.2213588 |
| cnvi0111198 |
NC |
0 |
0.963815 |
1.007221 |
0.9929234 |
-0.3648422 |
| cnvi0111199 |
NC |
0 |
0.01323316 |
1.310022 |
0 |
0.04303133 |
| cnvi0111200 |
NC |
0 |
0.9906043 |
1.06258 |
1 |
0.2687665 |
| cnvi0111201 |
NC |
0 |
0.01656049 |
0.9434019 |
0 |
0.02855444 |
| cnvi0111202 |
NC |
0 |
0.9386989 |
1.428921 |
1 |
0.1000355 |
| cnvi0111203 |
NC |
0 |
0.03804795 |
1.551076 |
0.01377705 |
-0.09516481 |
| cnvi0111204 |
NC |
0 |
0.9820453 |
1.070034 |
0.9933782 |
-0.1873194 |
Total number of rows: 299140
Table truncated, full table size 17128 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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