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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_93 |
| 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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| |
|
| 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) |
[email protected]
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| Organization name |
The University of Chicago
|
| Department |
Health Studies
|
| 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 |
0.9806497 |
1.526912 |
1 |
0.07120247 |
| cnvi0111186 |
NC |
0 |
0.008837984 |
0.5534185 |
0 |
0.1522062 |
| cnvi0111187 |
NC |
0 |
0.9852837 |
1.354208 |
1 |
-0.1741673 |
| cnvi0111188 |
NC |
0 |
0.01112274 |
1.248635 |
0 |
-0.0637125 |
| cnvi0111189 |
NC |
0 |
0.0222343 |
1.453244 |
0 |
0.01096602 |
| cnvi0111190 |
NC |
0 |
0.004022735 |
0.4560991 |
0 |
0.3462176 |
| cnvi0111191 |
NC |
0 |
0.0210301 |
0.8555692 |
0 |
-0.3618748 |
| cnvi0111192 |
NC |
0 |
0.01895727 |
1.172775 |
0 |
0.07426667 |
| cnvi0111193 |
NC |
0 |
0.007806224 |
1.20906 |
0 |
-0.005938437 |
| cnvi0111194 |
NC |
0 |
0.9929407 |
1.224326 |
1 |
-0.1202067 |
| cnvi0111195 |
NC |
0 |
0.03446277 |
2.203261 |
0.002023255 |
0.1742488 |
| cnvi0111196 |
NC |
0 |
0.991253 |
1.174228 |
1 |
-0.06399743 |
| cnvi0111197 |
NC |
0 |
0.006919755 |
0.9946429 |
0 |
0.1560453 |
| cnvi0111198 |
NC |
0 |
0.9737127 |
1.087581 |
1 |
-0.2540985 |
| cnvi0111199 |
NC |
0 |
0.01216824 |
1.274626 |
0 |
0.003514563 |
| cnvi0111200 |
NC |
0 |
0.9877654 |
0.9206362 |
1 |
0.06189786 |
| cnvi0111201 |
NC |
0 |
0.02272138 |
0.7661957 |
0.004462023 |
-0.2716051 |
| cnvi0111202 |
NC |
0 |
0.9335681 |
1.420218 |
1 |
0.09122176 |
| cnvi0111203 |
NC |
0 |
0.04130577 |
1.712684 |
0.0172039 |
0.04782445 |
| cnvi0111204 |
NC |
0 |
0.9844637 |
1.273958 |
0.9958877 |
0.06434184 |
Total number of rows: 299140
Table truncated, full table size 17203 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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