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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_115 |
| 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.
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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
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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 |
0.9846397 |
1.256755 |
1 |
-0.2097109 |
| cnvi0111186 |
NC |
0 |
0.004844725 |
0.5290378 |
0 |
0.08720618 |
| cnvi0111187 |
NC |
0 |
0.9867594 |
1.34524 |
1 |
-0.1837527 |
| cnvi0111188 |
NC |
0 |
0.007697695 |
1.1862 |
0 |
-0.1377168 |
| cnvi0111189 |
NC |
0 |
0.02092098 |
1.455072 |
0 |
0.01277968 |
| cnvi0111190 |
NC |
0 |
0.0001708246 |
0.5221932 |
0 |
0.5414539 |
| cnvi0111191 |
NC |
0 |
0.0263425 |
1.09529 |
0 |
-0.005518899 |
| cnvi0111192 |
NC |
0 |
0.01772792 |
1.118663 |
0 |
0.006115789 |
| cnvi0111193 |
NC |
0 |
0.005876248 |
1.156745 |
0 |
-0.06975269 |
| cnvi0111194 |
NC |
0 |
0.9850527 |
1.254722 |
1 |
-0.08482723 |
| cnvi0111195 |
NC |
0 |
0.02752776 |
2.062377 |
0 |
0.07891647 |
| cnvi0111196 |
NC |
0 |
0.9847515 |
1.167498 |
1 |
-0.07229075 |
| cnvi0111197 |
NC |
0 |
0.003822261 |
1.026479 |
0 |
0.201499 |
| cnvi0111198 |
NC |
0 |
0.9794381 |
1.107107 |
1 |
-0.2284272 |
| cnvi0111199 |
NC |
0 |
0.01208166 |
1.268685 |
0 |
-0.003225968 |
| cnvi0111200 |
NC |
0 |
0.994556 |
0.9374319 |
1 |
0.08798057 |
| cnvi0111201 |
NC |
0 |
0.01899442 |
0.7876076 |
0.0005676434 |
-0.2318411 |
| cnvi0111202 |
NC |
0 |
0.9316947 |
1.275884 |
1 |
-0.06339408 |
| cnvi0111203 |
NC |
0 |
0.04724146 |
1.846981 |
0.02344757 |
0.1567348 |
| cnvi0111204 |
NC |
0 |
0.9913222 |
1.198438 |
1 |
-0.02382038 |
Total number of rows: 299140
Table truncated, full table size 17088 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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