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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_79 |
| 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
|
| 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 |
0.9765203 |
1.31453 |
1 |
-0.1448676 |
| cnvi0111186 |
NC |
0 |
0.01607198 |
0.4996653 |
0 |
0.004797365 |
| cnvi0111187 |
NC |
0 |
0.9833568 |
1.433878 |
0.9981363 |
-0.0916943 |
| cnvi0111188 |
NC |
0 |
0.009406529 |
1.40237 |
0 |
0.1038026 |
| cnvi0111189 |
NC |
0 |
0.02561223 |
1.446335 |
0 |
0.004090328 |
| cnvi0111190 |
NC |
0 |
0.005507483 |
0.5486805 |
0 |
0.6128365 |
| cnvi0111191 |
NC |
0 |
0.02805589 |
1.431831 |
0 |
0.3810302 |
| cnvi0111192 |
NC |
0 |
0.01860958 |
1.12232 |
0 |
0.01082452 |
| cnvi0111193 |
NC |
0 |
0.004405412 |
1.108409 |
0 |
-0.1313339 |
| cnvi0111194 |
NC |
0 |
0.9935122 |
1.242739 |
1 |
-0.0986717 |
| cnvi0111195 |
NC |
0 |
0.03026603 |
2.009434 |
0 |
0.04139793 |
| cnvi0111196 |
NC |
0 |
0.9899856 |
0.9612406 |
1 |
-0.3527408 |
| cnvi0111197 |
NC |
0 |
0.01079846 |
1.041699 |
0 |
0.2227339 |
| cnvi0111198 |
NC |
0 |
0.9729058 |
1.148661 |
1 |
-0.1752685 |
| cnvi0111199 |
NC |
0 |
0.009940782 |
1.386447 |
0 |
0.1248336 |
| cnvi0111200 |
NC |
0 |
0.9952472 |
0.9426414 |
1 |
0.09597573 |
| cnvi0111201 |
NC |
0 |
0.03914538 |
0.6884612 |
0.02162381 |
-0.4259426 |
| cnvi0111202 |
NC |
0 |
0.9463317 |
1.338617 |
1 |
0.005852844 |
| cnvi0111203 |
NC |
0 |
0.04382921 |
1.994046 |
0.01985827 |
0.2672639 |
| cnvi0111204 |
NC |
0 |
0.9891683 |
1.212967 |
1 |
-0.006435788 |
Total number of rows: 299140
Table truncated, full table size 17196 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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