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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_95 |
| 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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| 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 |
0.982026 |
1.460345 |
1 |
0.006895427 |
| cnvi0111186 |
NC |
0 |
0.005012181 |
0.5482597 |
0 |
0.138695 |
| cnvi0111187 |
NC |
0 |
0.9897887 |
1.567501 |
1 |
0.0368497 |
| cnvi0111188 |
NC |
0 |
0.009765225 |
1.420682 |
0 |
0.1225191 |
| cnvi0111189 |
NC |
0 |
0.01593701 |
1.583441 |
0 |
0.1347523 |
| cnvi0111190 |
NC |
0 |
0 |
0.4027448 |
0 |
0.1667362 |
| cnvi0111191 |
NC |
0 |
0.02265763 |
1.069335 |
0 |
-0.04011707 |
| cnvi0111192 |
NC |
0 |
0.0145094 |
1.086506 |
0 |
-0.03596318 |
| cnvi0111193 |
NC |
0 |
0.005966172 |
1.116583 |
0 |
-0.120733 |
| cnvi0111194 |
NC |
0 |
0.9894173 |
1.242528 |
1 |
-0.09891597 |
| cnvi0111195 |
NC |
0 |
0.02696167 |
2.344993 |
0 |
0.2641918 |
| cnvi0111196 |
NC |
0 |
0.9928054 |
1.116606 |
1 |
-0.1365906 |
| cnvi0111197 |
NC |
0 |
0.001824895 |
0.8907861 |
0 |
-0.003054293 |
| cnvi0111198 |
NC |
0 |
0.9787028 |
1.268193 |
1 |
-0.0324473 |
| cnvi0111199 |
NC |
0 |
0.008791248 |
1.328565 |
0 |
0.0633095 |
| cnvi0111200 |
NC |
0 |
0.9939314 |
0.8811532 |
1 |
-0.00134055 |
| cnvi0111201 |
NC |
0 |
0.01492148 |
0.6889588 |
0 |
-0.4249004 |
| cnvi0111202 |
NC |
0 |
0.9370745 |
1.38491 |
1 |
0.05490159 |
| cnvi0111203 |
NC |
0 |
0.03747635 |
2.042486 |
0.01317579 |
0.3018916 |
| cnvi0111204 |
NC |
0 |
0.9900529 |
1.304793 |
1 |
0.09884576 |
Total number of rows: 299140
Table truncated, full table size 16977 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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