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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_159 |
| 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) |
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 |
0.9770982 |
1.128016 |
1 |
-0.3656271 |
| cnvi0111186 |
NC |
0 |
0.01199634 |
0.5463303 |
0 |
0.133609 |
| cnvi0111187 |
NC |
0 |
0.9882056 |
1.476638 |
1 |
-0.04930002 |
| cnvi0111188 |
NC |
0 |
0.009726495 |
1.266109 |
0 |
-0.04366318 |
| cnvi0111189 |
NC |
0 |
0.02526223 |
1.344774 |
0 |
-0.1009468 |
| cnvi0111190 |
NC |
0 |
0.003223263 |
0.586112 |
0 |
0.7080467 |
| cnvi0111191 |
NC |
0 |
0.03046769 |
0.5606033 |
0.001910443 |
-0.9717792 |
| cnvi0111192 |
NC |
0 |
0.0172981 |
1.063958 |
0 |
-0.06621855 |
| cnvi0111193 |
NC |
0 |
0.008290587 |
1.214031 |
0 |
-1.8416E-05 |
| cnvi0111194 |
NC |
0 |
0.9912732 |
1.305605 |
1 |
-0.02747603 |
| cnvi0111195 |
NC |
0 |
0.02851032 |
2.213922 |
0 |
0.1812125 |
| cnvi0111196 |
NC |
0 |
0.9857343 |
1.112095 |
1 |
-0.14243 |
| cnvi0111197 |
NC |
0 |
0.01038162 |
1.009075 |
0 |
0.1768278 |
| cnvi0111198 |
NC |
0 |
0.9738908 |
1.265229 |
1 |
-0.03582393 |
| cnvi0111199 |
NC |
0 |
0.00875107 |
1.497901 |
0 |
0.2363829 |
| cnvi0111200 |
NC |
0 |
0.9966214 |
0.8456551 |
1 |
-0.06066391 |
| cnvi0111201 |
NC |
0 |
0.02188331 |
0.8234724 |
0.003586307 |
-0.1675978 |
| cnvi0111202 |
NC |
0 |
0.9365634 |
1.390651 |
1 |
0.06087014 |
| cnvi0111203 |
NC |
0 |
0.02738517 |
1.830586 |
0.002561016 |
0.1438708 |
| cnvi0111204 |
NC |
0 |
0.9863726 |
1.153491 |
0.9978684 |
-0.07896953 |
Total number of rows: 299140
Table truncated, full table size 17202 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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