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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_157 |
| Sample type |
genomic |
| |
|
| 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
|
| Street address |
900 E 57th Street
|
| 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 |
0.9675316 |
1.373885 |
0.9923085 |
-0.08115304 |
| cnvi0111186 |
NC |
0 |
0.01266236 |
0.5628565 |
0 |
0.1766026 |
| cnvi0111187 |
NC |
0 |
0.9849074 |
1.569346 |
0.9997507 |
0.03854691 |
| cnvi0111188 |
NC |
0 |
0.01391664 |
1.262788 |
0 |
-0.04745226 |
| cnvi0111189 |
NC |
0 |
0.02989166 |
1.45347 |
0.003735637 |
0.01119074 |
| cnvi0111190 |
NC |
0 |
0 |
0.532198 |
0 |
0.5688332 |
| cnvi0111191 |
NC |
0 |
0.04206187 |
0.6171413 |
0.01415275 |
-0.8331585 |
| cnvi0111192 |
NC |
0 |
0.02173179 |
1.131589 |
0 |
0.02269095 |
| cnvi0111193 |
NC |
0 |
0.0131817 |
1.249397 |
0 |
0.04140753 |
| cnvi0111194 |
NC |
0 |
0.9894753 |
1.208075 |
1 |
-0.1394852 |
| cnvi0111195 |
NC |
0 |
0.03972841 |
2.147804 |
0.007605649 |
0.1374708 |
| cnvi0111196 |
NC |
0 |
0.9802352 |
1.221805 |
0.9967536 |
-0.006696208 |
| cnvi0111197 |
NC |
0 |
0.009319129 |
1.039596 |
0 |
0.2198174 |
| cnvi0111198 |
NC |
0 |
0.9667882 |
1.162374 |
0.9960656 |
-0.1581478 |
| cnvi0111199 |
NC |
0 |
0.01286318 |
1.341284 |
0 |
0.07705547 |
| cnvi0111200 |
NC |
0 |
0.9920635 |
0.9549141 |
1 |
0.1146376 |
| cnvi0111201 |
NC |
0 |
0.02580189 |
0.87709 |
0.007680915 |
-0.07659307 |
| cnvi0111202 |
NC |
0 |
0.9317636 |
1.273668 |
1 |
-0.06590115 |
| cnvi0111203 |
NC |
0 |
0.04893427 |
1.90311 |
0.02522822 |
0.199924 |
| cnvi0111204 |
NC |
0 |
0.9888647 |
1.18211 |
1 |
-0.04361133 |
Total number of rows: 299140
Table truncated, full table size 17490 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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