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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_120 |
| 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
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
|
| 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
|
| Street address |
900 E 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| 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 |
0.9807131 |
1.345945 |
1 |
-0.1107947 |
| cnvi0111186 |
NC |
0 |
0.002889085 |
0.5418833 |
0 |
0.1218176 |
| cnvi0111187 |
NC |
0 |
0.985041 |
1.458464 |
0.9998897 |
-0.06716684 |
| cnvi0111188 |
NC |
0 |
0.007659166 |
1.368588 |
0 |
0.06862417 |
| cnvi0111189 |
NC |
0 |
0.02488442 |
1.494623 |
0 |
0.05147056 |
| cnvi0111190 |
NC |
0 |
0 |
0.5104135 |
0 |
0.5085366 |
| cnvi0111191 |
NC |
0 |
0.02554457 |
0.9702726 |
0 |
-0.1803692 |
| cnvi0111192 |
NC |
0 |
0.01765877 |
1.218893 |
0 |
0.1299121 |
| cnvi0111193 |
NC |
0 |
0.007034414 |
1.183391 |
0 |
-0.03689656 |
| cnvi0111194 |
NC |
0 |
0.9889897 |
1.246346 |
1 |
-0.09448981 |
| cnvi0111195 |
NC |
0 |
0.02837454 |
2.099861 |
0 |
0.104902 |
| cnvi0111196 |
NC |
0 |
0.9932028 |
1.059945 |
1 |
-0.2117203 |
| cnvi0111197 |
NC |
0 |
0.005069851 |
0.9965335 |
0 |
0.1587851 |
| cnvi0111198 |
NC |
0 |
0.9811176 |
1.237146 |
1 |
-0.06820652 |
| cnvi0111199 |
NC |
0 |
0.009443128 |
1.416417 |
0 |
0.1556866 |
| cnvi0111200 |
NC |
0 |
0.9898968 |
0.9925858 |
1 |
0.1704584 |
| cnvi0111201 |
NC |
0 |
0.01274323 |
0.7643594 |
0 |
-0.275067 |
| cnvi0111202 |
NC |
0 |
0.9335784 |
1.370497 |
1 |
0.03980791 |
| cnvi0111203 |
NC |
0 |
0.04231684 |
1.989646 |
0.01826743 |
0.2640773 |
| cnvi0111204 |
NC |
0 |
0.9949881 |
1.044065 |
1 |
-0.2227643 |
Total number of rows: 299140
Table truncated, full table size 17086 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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