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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_151 |
| 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
|
| 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 |
0.9793108 |
1.366569 |
1 |
-0.0888561 |
| cnvi0111186 |
NC |
0 |
0.009124783 |
0.4513575 |
0 |
-0.1418938 |
| cnvi0111187 |
NC |
0 |
0.9864146 |
1.512207 |
1 |
-0.01496051 |
| cnvi0111188 |
NC |
0 |
0.009427377 |
1.214468 |
0 |
-0.1037395 |
| cnvi0111189 |
NC |
0 |
0.02777235 |
1.457016 |
0.001503167 |
0.01470616 |
| cnvi0111190 |
NC |
0 |
0 |
0.5656271 |
0 |
0.6567215 |
| cnvi0111191 |
NC |
0 |
0.03430732 |
0.3636571 |
0.005964705 |
-1.596181 |
| cnvi0111192 |
NC |
0 |
0.02399109 |
1.136484 |
0 |
0.02891793 |
| cnvi0111193 |
NC |
0 |
0.006271278 |
1.099723 |
0 |
-0.1426835 |
| cnvi0111194 |
NC |
0 |
0.9866654 |
1.288965 |
1 |
-0.0459819 |
| cnvi0111195 |
NC |
0 |
0.0334569 |
1.969878 |
0.0009568795 |
0.01271475 |
| cnvi0111196 |
NC |
0 |
0.9870457 |
1.112458 |
1 |
-0.1419598 |
| cnvi0111197 |
NC |
0 |
0.006225896 |
0.9674151 |
0 |
0.1160018 |
| cnvi0111198 |
NC |
0 |
0.9645472 |
1.044135 |
0.9936972 |
-0.3129138 |
| cnvi0111199 |
NC |
0 |
0.01522803 |
1.581961 |
0 |
0.315155 |
| cnvi0111200 |
NC |
0 |
0.9971287 |
0.8532533 |
1 |
-0.04775927 |
| cnvi0111201 |
NC |
0 |
0.02139372 |
0.7378693 |
0.003074727 |
-0.3259527 |
| cnvi0111202 |
NC |
0 |
0.9390703 |
1.281925 |
1 |
-0.05657853 |
| cnvi0111203 |
NC |
0 |
0.04840915 |
1.768424 |
0.02467585 |
0.09402938 |
| cnvi0111204 |
NC |
0 |
0.9908682 |
1.090863 |
1 |
-0.1595064 |
Total number of rows: 299140
Table truncated, full table size 17273 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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