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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_118 |
| 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
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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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| |
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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) |
[email protected]
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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 |
0.978301 |
1.344561 |
1 |
-0.1122789 |
| cnvi0111186 |
NC |
0 |
0.0080017 |
0.4639543 |
0 |
-0.1021819 |
| cnvi0111187 |
NC |
0 |
0.9867855 |
1.397346 |
1 |
-0.128927 |
| cnvi0111188 |
NC |
0 |
0.01002835 |
1.364758 |
0 |
0.06458104 |
| cnvi0111189 |
NC |
0 |
0.02336294 |
1.523144 |
0 |
0.07874178 |
| cnvi0111190 |
NC |
0 |
0 |
0.5095021 |
0 |
0.5059582 |
| cnvi0111191 |
NC |
0 |
0.02415744 |
0.8504127 |
0 |
-0.3705962 |
| cnvi0111192 |
NC |
0 |
0.01929173 |
1.097315 |
0 |
-0.02168151 |
| cnvi0111193 |
NC |
0 |
0.006333536 |
1.124522 |
0 |
-0.1105122 |
| cnvi0111194 |
NC |
0 |
0.9895203 |
1.227995 |
1 |
-0.1158901 |
| cnvi0111195 |
NC |
0 |
0.03289234 |
2.104377 |
0.0003583549 |
0.1080018 |
| cnvi0111196 |
NC |
0 |
0.9900352 |
1.247585 |
1 |
0.02342781 |
| cnvi0111197 |
NC |
0 |
0.003723613 |
1.090865 |
0 |
0.2892676 |
| cnvi0111198 |
NC |
0 |
0.9645168 |
1.257435 |
0.9936651 |
-0.04473798 |
| cnvi0111199 |
NC |
0 |
0.008911527 |
1.352038 |
0 |
0.08857667 |
| cnvi0111200 |
NC |
0 |
0.9991073 |
0.924668 |
1 |
0.06820212 |
| cnvi0111201 |
NC |
0 |
0.01255893 |
0.7452148 |
0 |
-0.3116617 |
| cnvi0111202 |
NC |
0 |
0.9322656 |
1.361977 |
1 |
0.03081145 |
| cnvi0111203 |
NC |
0 |
0.05198407 |
2.03377 |
0.02843626 |
0.2957219 |
| cnvi0111204 |
NC |
0 |
0.9928796 |
1.176313 |
1 |
-0.05070323 |
Total number of rows: 299140
Table truncated, full table size 17115 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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