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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_58 |
| 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.
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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 |
0.9759267 |
1.493089 |
1 |
0.03888604 |
| cnvi0111186 |
NC |
0 |
0.01649199 |
0.5245338 |
0 |
0.07487121 |
| cnvi0111187 |
NC |
0 |
0.98254 |
1.607832 |
0.9972859 |
0.07350012 |
| cnvi0111188 |
NC |
0 |
0.009611705 |
1.341589 |
0 |
0.03987848 |
| cnvi0111189 |
NC |
0 |
0.0212047 |
1.485752 |
0 |
0.04288275 |
| cnvi0111190 |
NC |
0 |
0.001678399 |
0.4883093 |
0 |
0.4446655 |
| cnvi0111191 |
NC |
0 |
0.04853389 |
0.2175677 |
0.02098657 |
-2.337295 |
| cnvi0111192 |
NC |
0 |
0.01315305 |
1.134215 |
0 |
0.02603451 |
| cnvi0111193 |
NC |
0 |
0.009101874 |
0.9940619 |
0 |
-0.2884164 |
| cnvi0111194 |
NC |
0 |
0.9894453 |
1.108993 |
1 |
-0.2629439 |
| cnvi0111195 |
NC |
0 |
0.03207132 |
2.172866 |
0 |
0.1542074 |
| cnvi0111196 |
NC |
0 |
0.9841327 |
1.134929 |
1 |
-0.1131078 |
| cnvi0111197 |
NC |
0 |
0.007511145 |
0.7985045 |
0 |
-0.1608328 |
| cnvi0111198 |
NC |
0 |
0.9736329 |
1.316229 |
1 |
0.02118847 |
| cnvi0111199 |
NC |
0 |
0.007390981 |
1.326789 |
0 |
0.06137915 |
| cnvi0111200 |
NC |
0 |
0.9986851 |
0.8941047 |
1 |
0.01971045 |
| cnvi0111201 |
NC |
0 |
0.02166714 |
0.9181116 |
0.003360423 |
-0.01064846 |
| cnvi0111202 |
NC |
0 |
0.9216626 |
1.407505 |
0.995612 |
0.07824958 |
| cnvi0111203 |
NC |
0 |
0.03011522 |
1.478502 |
0.005432721 |
-0.1642987 |
| cnvi0111204 |
NC |
0 |
0.9898108 |
1.157105 |
1 |
-0.07445596 |
Total number of rows: 299140
Table truncated, full table size 17267 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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