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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_165 |
| Sample type |
genomic |
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| Source name |
Colon tissue, normal
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: normal colon mucosa
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| 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
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| 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 |
0.975356 |
1.324406 |
1 |
-0.1340691 |
| cnvi0111186 |
NC |
0 |
0.01254854 |
0.4998372 |
0 |
0.005293696 |
| cnvi0111187 |
NC |
0 |
0.990398 |
1.552859 |
1 |
0.02331017 |
| cnvi0111188 |
NC |
0 |
0.008590492 |
1.370612 |
0 |
0.07075574 |
| cnvi0111189 |
NC |
0 |
0.02778417 |
1.417933 |
0.001515624 |
-0.02452191 |
| cnvi0111190 |
NC |
0 |
0.004042025 |
0.5252185 |
0 |
0.5497879 |
| cnvi0111191 |
NC |
0 |
0.03489722 |
0.6659039 |
0.006587581 |
-0.7234454 |
| cnvi0111192 |
NC |
0 |
0.02086002 |
1.114614 |
0 |
0.0008850158 |
| cnvi0111193 |
NC |
0 |
0.007005434 |
1.169153 |
0 |
-0.05436052 |
| cnvi0111194 |
NC |
0 |
0.9906549 |
1.218483 |
1 |
-0.1271081 |
| cnvi0111195 |
NC |
0 |
0.03230894 |
2.274038 |
0 |
0.2198648 |
| cnvi0111196 |
NC |
0 |
0.9857436 |
1.156525 |
1 |
-0.08591346 |
| cnvi0111197 |
NC |
0 |
0.01653564 |
0.8965821 |
0.003984263 |
0.006302383 |
| cnvi0111198 |
NC |
0 |
0.969263 |
1.536742 |
0.9986808 |
0.2446527 |
| cnvi0111199 |
NC |
0 |
0.01175939 |
1.43427 |
0 |
0.1737571 |
| cnvi0111200 |
NC |
0 |
0.9892796 |
0.9107801 |
1 |
0.04636936 |
| cnvi0111201 |
NC |
0 |
0.01169171 |
0.8584225 |
0 |
-0.1076301 |
| cnvi0111202 |
NC |
0 |
0.942865 |
1.468863 |
1 |
0.1398095 |
| cnvi0111203 |
NC |
0 |
0.0305597 |
1.843271 |
0.005900264 |
0.1538334 |
| cnvi0111204 |
NC |
0 |
0.9915359 |
1.223536 |
1 |
0.006081139 |
Total number of rows: 299140
Table truncated, full table size 17266 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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