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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_162 |
| 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 |
0.9758435 |
1.401689 |
1 |
-0.05224786 |
| cnvi0111186 |
NC |
0 |
0.01012689 |
0.53445 |
0 |
0.1018904 |
| cnvi0111187 |
NC |
0 |
0.9799439 |
1.494731 |
0.9945832 |
-0.03173069 |
| cnvi0111188 |
NC |
0 |
0.007483049 |
1.280763 |
0 |
-0.02706107 |
| cnvi0111189 |
NC |
0 |
0.02183064 |
1.490814 |
0 |
0.04778945 |
| cnvi0111190 |
NC |
0 |
0.00172755 |
0.5966331 |
0 |
0.7337142 |
| cnvi0111191 |
NC |
0 |
0.02609513 |
1.129116 |
0 |
0.03836268 |
| cnvi0111192 |
NC |
0 |
0.02005026 |
1.199674 |
0 |
0.1069833 |
| cnvi0111193 |
NC |
0 |
0.008661342 |
1.180488 |
0 |
-0.04044072 |
| cnvi0111194 |
NC |
0 |
0.9892868 |
1.240397 |
1 |
-0.1013922 |
| cnvi0111195 |
NC |
0 |
0.03036127 |
2.251695 |
0 |
0.2056199 |
| cnvi0111196 |
NC |
0 |
0.9915785 |
1.229492 |
1 |
0.002351918 |
| cnvi0111197 |
NC |
0 |
0.01265831 |
0.9744959 |
0 |
0.1265229 |
| cnvi0111198 |
NC |
0 |
0.9696553 |
1.543702 |
0.9990954 |
0.2511721 |
| cnvi0111199 |
NC |
0 |
0.006870621 |
1.522919 |
0 |
0.2602798 |
| cnvi0111200 |
NC |
0 |
0.9895709 |
0.8861518 |
1 |
0.006820475 |
| cnvi0111201 |
NC |
0 |
0.02645073 |
0.9182494 |
0.0083589 |
-0.01043193 |
| cnvi0111202 |
NC |
0 |
0.9437076 |
1.586978 |
1 |
0.2513918 |
| cnvi0111203 |
NC |
0 |
0.03841777 |
1.875132 |
0.01416605 |
0.1785576 |
| cnvi0111204 |
NC |
0 |
0.9904786 |
1.360584 |
1 |
0.1592508 |
Total number of rows: 299140
Table truncated, full table size 17243 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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