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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_166 |
| 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
|
| 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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| |
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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 |
0.9713038 |
1.536984 |
0.9962773 |
0.08068792 |
| cnvi0111186 |
NC |
0 |
0.009422807 |
0.5602522 |
0 |
0.169912 |
| cnvi0111187 |
NC |
0 |
0.9928378 |
1.422694 |
1 |
-0.1029907 |
| cnvi0111188 |
NC |
0 |
0.0144151 |
1.351353 |
0 |
0.05034013 |
| cnvi0111189 |
NC |
0 |
0.02567901 |
1.496854 |
0 |
0.05362221 |
| cnvi0111190 |
NC |
0 |
0.009358761 |
0.4638654 |
0 |
0.3705766 |
| cnvi0111191 |
NC |
0 |
0.05369489 |
0.3563837 |
0.02643607 |
-1.625328 |
| cnvi0111192 |
NC |
0 |
0.0202583 |
1.031921 |
0 |
-0.1103266 |
| cnvi0111193 |
NC |
0 |
0.006179943 |
1.23154 |
0 |
0.02063909 |
| cnvi0111194 |
NC |
0 |
0.9866005 |
1.116181 |
1 |
-0.2536241 |
| cnvi0111195 |
NC |
0 |
0.0344249 |
2.389755 |
0.001983114 |
0.2914711 |
| cnvi0111196 |
NC |
0 |
0.9865784 |
1.127447 |
1 |
-0.1226512 |
| cnvi0111197 |
NC |
0 |
0.00864199 |
0.9913109 |
0 |
0.1512043 |
| cnvi0111198 |
NC |
0 |
0.9758417 |
1.268672 |
1 |
-0.03190251 |
| cnvi0111199 |
NC |
0 |
0.009228747 |
1.352398 |
0 |
0.08896051 |
| cnvi0111200 |
NC |
0 |
0.9966789 |
0.8892691 |
1 |
0.01188661 |
| cnvi0111201 |
NC |
0 |
0.02899416 |
0.8358824 |
0.01101658 |
-0.1460181 |
| cnvi0111202 |
NC |
0 |
0.9380324 |
1.274338 |
1 |
-0.06514249 |
| cnvi0111203 |
NC |
0 |
0.03633017 |
1.855189 |
0.01197014 |
0.1631315 |
| cnvi0111204 |
NC |
0 |
0.9864348 |
1.329847 |
0.997933 |
0.1262847 |
Total number of rows: 299140
Table truncated, full table size 17298 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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