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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_156 |
| 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
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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
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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 |
0.9734707 |
1.508838 |
0.9985571 |
0.05402343 |
| cnvi0111186 |
NC |
0 |
0.01042264 |
0.5938799 |
0 |
0.2540067 |
| cnvi0111187 |
NC |
0 |
0.9832694 |
1.572166 |
0.9980453 |
0.0411369 |
| cnvi0111188 |
NC |
0 |
0.007954213 |
1.344518 |
0 |
0.04302438 |
| cnvi0111189 |
NC |
0 |
0.02175233 |
1.408361 |
0 |
-0.03429364 |
| cnvi0111190 |
NC |
0 |
0.00757893 |
0.5699072 |
0 |
0.6675974 |
| cnvi0111191 |
NC |
0 |
0.03321714 |
0.6783459 |
0.00481359 |
-0.6967382 |
| cnvi0111192 |
NC |
0 |
0.01836272 |
1.179642 |
0 |
0.08269046 |
| cnvi0111193 |
NC |
0 |
0.00891866 |
1.194217 |
0 |
-0.02375839 |
| cnvi0111194 |
NC |
0 |
0.9949293 |
1.319053 |
1 |
-0.01269264 |
| cnvi0111195 |
NC |
0 |
0.03650009 |
2.181637 |
0.004183128 |
0.1600195 |
| cnvi0111196 |
NC |
0 |
0.9893854 |
1.191415 |
1 |
-0.04303368 |
| cnvi0111197 |
NC |
0 |
0.0169937 |
1.044003 |
0.004460119 |
0.2259205 |
| cnvi0111198 |
NC |
0 |
0.970634 |
1.245992 |
1 |
-0.05792729 |
| cnvi0111199 |
NC |
0 |
0.009977333 |
1.388093 |
0 |
0.1265448 |
| cnvi0111200 |
NC |
0 |
0.9896606 |
0.8735487 |
1 |
-0.01384525 |
| cnvi0111201 |
NC |
0 |
0.02272801 |
0.9131939 |
0.004468954 |
-0.01839683 |
| cnvi0111202 |
NC |
0 |
0.9423958 |
1.305889 |
1 |
-0.02985873 |
| cnvi0111203 |
NC |
0 |
0.0455673 |
1.986148 |
0.02168655 |
0.2615387 |
| cnvi0111204 |
NC |
0 |
0.9876207 |
1.180361 |
0.9991636 |
-0.04574737 |
Total number of rows: 299140
Table truncated, full table size 17221 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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