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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_73 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
|
| 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
|
| 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 |
0.966274 |
1.23999 |
0.9909853 |
-0.2290861 |
| cnvi0111186 |
NC |
0 |
0.02632447 |
0.18303 |
0 |
-1.444085 |
| cnvi0111187 |
NC |
0 |
0.9870061 |
1.702879 |
1 |
0.1563598 |
| cnvi0111188 |
NC |
0 |
0.01189669 |
1.23852 |
0 |
-0.07544786 |
| cnvi0111189 |
NC |
0 |
0.02881355 |
1.32214 |
0.002599959 |
-0.1254365 |
| cnvi0111190 |
NC |
0 |
0 |
0.5154051 |
0 |
0.5225771 |
| cnvi0111191 |
NC |
0 |
0.02759323 |
1.347147 |
0 |
0.2930761 |
| cnvi0111192 |
NC |
0 |
0.02421896 |
1.763779 |
0 |
0.6630105 |
| cnvi0111193 |
NC |
0 |
0.01393391 |
0.584731 |
0.0001406593 |
-1.053979 |
| cnvi0111194 |
NC |
0 |
0.9826606 |
1.863914 |
0.9997481 |
0.4861405 |
| cnvi0111195 |
NC |
0 |
0.03393658 |
2.314167 |
0.001465413 |
0.2451014 |
| cnvi0111196 |
NC |
0 |
0.997322 |
1.152447 |
1 |
-0.09101044 |
| cnvi0111197 |
NC |
0 |
0.00540656 |
1.174256 |
0 |
0.3955416 |
| cnvi0111198 |
NC |
0 |
0.9564013 |
1.453844 |
0.9850886 |
0.1646506 |
| cnvi0111199 |
NC |
0 |
0.02110238 |
2.417757 |
0.003806755 |
0.9271101 |
| cnvi0111200 |
NC |
0 |
0.987081 |
0.8133071 |
1 |
-0.1169331 |
| cnvi0111201 |
NC |
0 |
0.03547003 |
0.6017256 |
0.01778336 |
-0.6202122 |
| cnvi0111202 |
NC |
0 |
0.9285443 |
1.925194 |
1 |
0.5301127 |
| cnvi0111203 |
NC |
0 |
0.03418765 |
1.460829 |
0.009716451 |
-0.1816475 |
| cnvi0111204 |
NC |
0 |
0.991608 |
1.443563 |
1 |
0.2446588 |
Total number of rows: 299140
Table truncated, full table size 17340 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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