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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_155 |
| 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
|
| 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 |
0.9689028 |
1.368146 |
0.9937512 |
-0.08719206 |
| cnvi0111186 |
NC |
0 |
0.01562143 |
0.6338789 |
0 |
0.3480427 |
| cnvi0111187 |
NC |
0 |
0.9841341 |
1.318922 |
0.9989457 |
-0.2122574 |
| cnvi0111188 |
NC |
0 |
0.01510374 |
1.370866 |
0.0003736367 |
0.07102311 |
| cnvi0111189 |
NC |
0 |
0.02660535 |
1.581711 |
0.0002738558 |
0.1331752 |
| cnvi0111190 |
NC |
0 |
0.009873648 |
0.4758278 |
0 |
0.4073098 |
| cnvi0111191 |
NC |
0 |
0.06227408 |
0.3590105 |
0.03549485 |
-1.614733 |
| cnvi0111192 |
NC |
0 |
0.02085363 |
1.168558 |
0 |
0.06907076 |
| cnvi0111193 |
NC |
0 |
0.01127774 |
1.198885 |
0 |
-0.01813113 |
| cnvi0111194 |
NC |
0 |
0.982824 |
1.215389 |
0.9999185 |
-0.1307766 |
| cnvi0111195 |
NC |
0 |
0.04068983 |
2.05913 |
0.008624901 |
0.07664362 |
| cnvi0111196 |
NC |
0 |
0.9906689 |
1.145624 |
1 |
-0.09957611 |
| cnvi0111197 |
NC |
0 |
0.01222025 |
1.041114 |
0 |
0.2219233 |
| cnvi0111198 |
NC |
0 |
0.9715233 |
1.294737 |
1 |
-0.002562843 |
| cnvi0111199 |
NC |
0 |
0.00847568 |
1.428834 |
0 |
0.1682788 |
| cnvi0111200 |
NC |
0 |
0.9928141 |
0.8429033 |
1 |
-0.06536631 |
| cnvi0111201 |
NC |
0 |
0.02418295 |
0.8990871 |
0.005989254 |
-0.04085718 |
| cnvi0111202 |
NC |
0 |
0.9356852 |
1.264033 |
1 |
-0.07685693 |
| cnvi0111203 |
NC |
0 |
0.04537082 |
1.934081 |
0.02147988 |
0.2232135 |
| cnvi0111204 |
NC |
0 |
0.9893677 |
1.316558 |
1 |
0.111795 |
Total number of rows: 299140
Table truncated, full table size 17471 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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