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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_140 |
| 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
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| 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 |
0.9764021 |
1.325349 |
1 |
-0.1330422 |
| cnvi0111186 |
NC |
0 |
0.01249187 |
0.5618718 |
0 |
0.1740764 |
| cnvi0111187 |
NC |
0 |
0.9851768 |
1.541982 |
1 |
0.01316935 |
| cnvi0111188 |
NC |
0 |
0.01198911 |
1.275294 |
0 |
-0.03323415 |
| cnvi0111189 |
NC |
0 |
0.02687088 |
1.484251 |
0.0005535646 |
0.04142362 |
| cnvi0111190 |
NC |
0 |
0.002480704 |
0.4740528 |
0 |
0.401918 |
| cnvi0111191 |
NC |
0 |
0.03158813 |
1.032659 |
0.003093509 |
-0.09046775 |
| cnvi0111192 |
NC |
0 |
0.02428102 |
1.142611 |
0 |
0.03667473 |
| cnvi0111193 |
NC |
0 |
0.006820415 |
1.219653 |
0 |
0.006646683 |
| cnvi0111194 |
NC |
0 |
0.9849481 |
1.134096 |
1 |
-0.2306516 |
| cnvi0111195 |
NC |
0 |
0.03133468 |
2.254677 |
0 |
0.2075292 |
| cnvi0111196 |
NC |
0 |
0.9869084 |
0.9605268 |
1 |
-0.3538125 |
| cnvi0111197 |
NC |
0 |
0.01000901 |
0.9755239 |
0 |
0.1280439 |
| cnvi0111198 |
NC |
0 |
0.9762836 |
1.229666 |
1 |
-0.07695553 |
| cnvi0111199 |
NC |
0 |
0.007093558 |
1.333013 |
0 |
0.06813198 |
| cnvi0111200 |
NC |
0 |
0.9952873 |
0.860363 |
1 |
-0.03578787 |
| cnvi0111201 |
NC |
0 |
0.01678705 |
0.8843189 |
0 |
-0.06475122 |
| cnvi0111202 |
NC |
0 |
0.9430128 |
1.347923 |
1 |
0.01584776 |
| cnvi0111203 |
NC |
0 |
0.04605162 |
1.954619 |
0.022196 |
0.2384527 |
| cnvi0111204 |
NC |
0 |
0.9842464 |
1.196198 |
0.9956622 |
-0.02651894 |
Total number of rows: 299140
Table truncated, full table size 17285 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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