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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_147 |
| 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
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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 |
0.9660186 |
1.497615 |
0.9907166 |
0.04325223 |
| cnvi0111186 |
NC |
0 |
0.0620755 |
0.1674836 |
0.03381569 |
-1.572145 |
| cnvi0111187 |
NC |
0 |
0.9940634 |
2.052618 |
1 |
0.4258488 |
| cnvi0111188 |
NC |
0 |
0.01067663 |
1.101247 |
0 |
-0.2449265 |
| cnvi0111189 |
NC |
0 |
0.02870917 |
1.307753 |
0.00249001 |
-0.1412212 |
| cnvi0111190 |
NC |
0 |
0 |
0.4812429 |
0 |
0.4236355 |
| cnvi0111191 |
NC |
0 |
0.02932289 |
1.001927 |
0.0007016411 |
-0.1340535 |
| cnvi0111192 |
NC |
0 |
0.02331092 |
1.859434 |
0 |
0.7392045 |
| cnvi0111193 |
NC |
0 |
0.006253245 |
1.271582 |
0 |
0.06680057 |
| cnvi0111194 |
NC |
0 |
0.9830601 |
1.85191 |
1 |
0.4768195 |
| cnvi0111195 |
NC |
0 |
0.03607728 |
2.208712 |
0.003734885 |
0.1778139 |
| cnvi0111196 |
NC |
0 |
0.9935975 |
1.11502 |
1 |
-0.1386406 |
| cnvi0111197 |
NC |
0 |
0.01252526 |
0.991576 |
0 |
0.15159 |
| cnvi0111198 |
NC |
0 |
0.9631413 |
1.388795 |
0.9922115 |
0.09861203 |
| cnvi0111199 |
NC |
0 |
0.02044224 |
2.09061 |
0.003117662 |
0.7173645 |
| cnvi0111200 |
NC |
0 |
0.9897203 |
0.961455 |
1 |
0.124486 |
| cnvi0111201 |
NC |
0 |
0.03233273 |
0.6770395 |
0.01450513 |
-0.450078 |
| cnvi0111202 |
NC |
0 |
0.9419523 |
1.719168 |
1 |
0.3668195 |
| cnvi0111203 |
NC |
0 |
0.03362864 |
1.899809 |
0.00912844 |
0.1974197 |
| cnvi0111204 |
NC |
0 |
0.9971891 |
1.63546 |
1 |
0.4247206 |
Total number of rows: 299140
Table truncated, full table size 17448 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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