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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_158 |
| 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
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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 |
0.9668338 |
1.374369 |
0.9915743 |
-0.08064514 |
| cnvi0111186 |
NC |
0 |
0.01741271 |
0.5488171 |
0 |
0.1401609 |
| cnvi0111187 |
NC |
0 |
0.9859737 |
1.432314 |
1 |
-0.09326868 |
| cnvi0111188 |
NC |
0 |
0.01396692 |
1.306009 |
0 |
0.001100653 |
| cnvi0111189 |
NC |
0 |
0.03094221 |
1.468502 |
0.004842276 |
0.02603425 |
| cnvi0111190 |
NC |
0 |
0.00246992 |
0.590858 |
0 |
0.7196816 |
| cnvi0111191 |
NC |
0 |
0.03673927 |
0.649019 |
0.00853261 |
-0.7604986 |
| cnvi0111192 |
NC |
0 |
0.02233949 |
1.184129 |
0 |
0.08816694 |
| cnvi0111193 |
NC |
0 |
0.0112998 |
1.23821 |
0 |
0.02843162 |
| cnvi0111194 |
NC |
0 |
0.9813371 |
1.201966 |
0.998367 |
-0.1467983 |
| cnvi0111195 |
NC |
0 |
0.04225401 |
2.229009 |
0.01028317 |
0.1910106 |
| cnvi0111196 |
NC |
0 |
0.9816562 |
1.129478 |
0.9982357 |
-0.1200545 |
| cnvi0111197 |
NC |
0 |
0.01633281 |
1.058607 |
0.003773564 |
0.2459624 |
| cnvi0111198 |
NC |
0 |
0.975164 |
1.290675 |
1 |
-0.007096346 |
| cnvi0111199 |
NC |
0 |
0.01051432 |
1.447621 |
0 |
0.1871245 |
| cnvi0111200 |
NC |
0 |
0.9920829 |
0.9124698 |
1 |
0.04904345 |
| cnvi0111201 |
NC |
0 |
0.03514108 |
0.8163034 |
0.01743963 |
-0.1802125 |
| cnvi0111202 |
NC |
0 |
0.9329564 |
1.254703 |
1 |
-0.08754466 |
| cnvi0111203 |
NC |
0 |
0.04964201 |
1.818148 |
0.02597268 |
0.1340349 |
| cnvi0111204 |
NC |
0 |
0.9882891 |
1.11164 |
0.9998571 |
-0.1322865 |
Total number of rows: 299140
Table truncated, full table size 17631 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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