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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_102 |
| 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
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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 |
0.9811403 |
1.266404 |
1 |
-0.198676 |
| cnvi0111186 |
NC |
0 |
0.007133048 |
0.5342445 |
0 |
0.1013355 |
| cnvi0111187 |
NC |
0 |
0.9837737 |
1.46179 |
0.9985704 |
-0.06388072 |
| cnvi0111188 |
NC |
0 |
0.01090871 |
1.41362 |
0 |
0.1153303 |
| cnvi0111189 |
NC |
0 |
0.02626602 |
1.515576 |
0 |
0.07155518 |
| cnvi0111190 |
NC |
0 |
0 |
0.4073703 |
0 |
0.1832109 |
| cnvi0111191 |
NC |
0 |
0.01179274 |
0.3178447 |
0 |
-1.790437 |
| cnvi0111192 |
NC |
0 |
0.01673803 |
1.175204 |
0 |
0.07725237 |
| cnvi0111193 |
NC |
0 |
0.006437803 |
1.136086 |
0 |
-0.09575206 |
| cnvi0111194 |
NC |
0 |
0.9873604 |
1.117313 |
1 |
-0.2521616 |
| cnvi0111195 |
NC |
0 |
0.03219416 |
2.046396 |
0 |
0.06769411 |
| cnvi0111196 |
NC |
0 |
0.9876381 |
1.247007 |
1 |
0.0227599 |
| cnvi0111197 |
NC |
0 |
0.006397506 |
1.046462 |
0 |
0.229315 |
| cnvi0111198 |
NC |
0 |
0.9733313 |
1.249656 |
1 |
-0.05369107 |
| cnvi0111199 |
NC |
0 |
0.01523701 |
1.31112 |
0 |
0.04424085 |
| cnvi0111200 |
NC |
0 |
0.9895536 |
0.9765844 |
1 |
0.1470113 |
| cnvi0111201 |
NC |
0 |
0.01737997 |
0.7603986 |
0 |
-0.2825622 |
| cnvi0111202 |
NC |
0 |
0.9372905 |
1.416984 |
1 |
0.08793256 |
| cnvi0111203 |
NC |
0 |
0.04561054 |
1.834762 |
0.02173204 |
0.1471587 |
| cnvi0111204 |
NC |
0 |
0.9876881 |
1.170273 |
0.9992334 |
-0.0581311 |
Total number of rows: 299140
Table truncated, full table size 17158 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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