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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_152 |
| 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
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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 |
0.9736795 |
1.374028 |
0.9987768 |
-0.08100258 |
| cnvi0111186 |
NC |
0 |
0.01473665 |
0.4644284 |
0 |
-0.1007083 |
| cnvi0111187 |
NC |
0 |
0.9889997 |
1.341735 |
1 |
-0.1875172 |
| cnvi0111188 |
NC |
0 |
0.00796958 |
1.204635 |
0 |
-0.1154683 |
| cnvi0111189 |
NC |
0 |
0.03173822 |
1.503035 |
0.005680786 |
0.05956742 |
| cnvi0111190 |
NC |
0 |
0 |
0.5436793 |
0 |
0.5996261 |
| cnvi0111191 |
NC |
0 |
0.02389264 |
0.8339589 |
0 |
-0.398783 |
| cnvi0111192 |
NC |
0 |
0.02032424 |
1.167575 |
0 |
0.0678562 |
| cnvi0111193 |
NC |
0 |
0.00634939 |
1.212902 |
0 |
-0.001360867 |
| cnvi0111194 |
NC |
0 |
0.9850956 |
1.27053 |
1 |
-0.06676415 |
| cnvi0111195 |
NC |
0 |
0.03006685 |
2.173687 |
0 |
0.1547529 |
| cnvi0111196 |
NC |
0 |
0.9904813 |
1.222725 |
1 |
-0.005610363 |
| cnvi0111197 |
NC |
0 |
0.01050378 |
1.099982 |
0 |
0.3012746 |
| cnvi0111198 |
NC |
0 |
0.969408 |
1.287113 |
0.9988342 |
-0.01108296 |
| cnvi0111199 |
NC |
0 |
0.01451183 |
1.414857 |
0 |
0.1540965 |
| cnvi0111200 |
NC |
0 |
0.9964389 |
0.809604 |
1 |
-0.123517 |
| cnvi0111201 |
NC |
0 |
0.01977366 |
0.7471568 |
0.001381889 |
-0.307907 |
| cnvi0111202 |
NC |
0 |
0.9333014 |
1.36203 |
1 |
0.03086802 |
| cnvi0111203 |
NC |
0 |
0.0438268 |
1.980326 |
0.01985574 |
0.2573031 |
| cnvi0111204 |
NC |
0 |
0.9892128 |
1.258837 |
1 |
0.04711603 |
Total number of rows: 299140
Table truncated, full table size 17274 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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