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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_142 |
| 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.
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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
|
| 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 |
0.974633 |
1.191505 |
0.99978 |
-0.286629 |
| cnvi0111186 |
NC |
0 |
0.02110903 |
0.4675056 |
0 |
-0.0911808 |
| cnvi0111187 |
NC |
0 |
0.9917919 |
1.441674 |
1 |
-0.0838718 |
| cnvi0111188 |
NC |
0 |
0.008944618 |
1.22245 |
0 |
-0.09428903 |
| cnvi0111189 |
NC |
0 |
0.03022602 |
1.520494 |
0.004087843 |
0.07622898 |
| cnvi0111190 |
NC |
0 |
0.0003656061 |
0.5663128 |
0 |
0.6584695 |
| cnvi0111191 |
NC |
0 |
0.02787687 |
1.558495 |
0 |
0.5033225 |
| cnvi0111192 |
NC |
0 |
0.02206207 |
1.178021 |
0 |
0.08070617 |
| cnvi0111193 |
NC |
0 |
0.004665383 |
1.201408 |
0 |
-0.01509758 |
| cnvi0111194 |
NC |
0 |
0.9852004 |
1.141652 |
1 |
-0.2210712 |
| cnvi0111195 |
NC |
0 |
0.03087841 |
2.160341 |
0 |
0.1458676 |
| cnvi0111196 |
NC |
0 |
0.98864 |
1.196709 |
1 |
-0.03663809 |
| cnvi0111197 |
NC |
0 |
0.009535378 |
1.018123 |
0 |
0.1897071 |
| cnvi0111198 |
NC |
0 |
0.9701268 |
1.229145 |
0.9995938 |
-0.07756644 |
| cnvi0111199 |
NC |
0 |
0.0113199 |
1.529408 |
0 |
0.2664137 |
| cnvi0111200 |
NC |
0 |
0.9964937 |
0.8110948 |
1 |
-0.1208629 |
| cnvi0111201 |
NC |
0 |
0.01847556 |
0.75214 |
2.548118E-05 |
-0.2983168 |
| cnvi0111202 |
NC |
0 |
0.937273 |
1.300239 |
1 |
-0.03611369 |
| cnvi0111203 |
NC |
0 |
0.04212843 |
1.830039 |
0.01806925 |
0.14344 |
| cnvi0111204 |
NC |
0 |
0.9853325 |
1.160066 |
0.9967892 |
-0.07076821 |
Total number of rows: 299140
Table truncated, full table size 17256 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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