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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_117 |
| 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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| Label |
C-Bio and A-DNP
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| 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 |
0.9759936 |
1.320794 |
1 |
-0.1380086 |
| cnvi0111186 |
NC |
0 |
0.01170161 |
0.5546084 |
0 |
0.1553049 |
| cnvi0111187 |
NC |
0 |
0.9850119 |
1.549987 |
0.9998595 |
0.0206399 |
| cnvi0111188 |
NC |
0 |
0.009074689 |
1.286884 |
0 |
-0.02018242 |
| cnvi0111189 |
NC |
0 |
0.02384005 |
1.507178 |
0 |
0.0635384 |
| cnvi0111190 |
NC |
0 |
0 |
0.4198296 |
0 |
0.2266742 |
| cnvi0111191 |
NC |
0 |
0.02706678 |
0.9203602 |
0 |
-0.2565607 |
| cnvi0111192 |
NC |
0 |
0.01557118 |
1.16008 |
0 |
0.05856477 |
| cnvi0111193 |
NC |
0 |
0.01005511 |
1.169394 |
0 |
-0.05406238 |
| cnvi0111194 |
NC |
0 |
0.983293 |
1.339358 |
1 |
0.009346896 |
| cnvi0111195 |
NC |
0 |
0.02861458 |
2.221267 |
0 |
0.1859915 |
| cnvi0111196 |
NC |
0 |
0.9874555 |
1.100155 |
1 |
-0.158003 |
| cnvi0111197 |
NC |
0 |
0.003421961 |
0.9957778 |
0 |
0.1576907 |
| cnvi0111198 |
NC |
0 |
0.968631 |
1.270107 |
0.998013 |
-0.03027141 |
| cnvi0111199 |
NC |
0 |
0.01307913 |
1.432761 |
0 |
0.1722382 |
| cnvi0111200 |
NC |
0 |
0.9900775 |
0.9238427 |
1 |
0.06691381 |
| cnvi0111201 |
NC |
0 |
0.0124824 |
0.8927603 |
0 |
-0.05104519 |
| cnvi0111202 |
NC |
0 |
0.9319113 |
1.431361 |
1 |
0.1024964 |
| cnvi0111203 |
NC |
0 |
0.04448242 |
1.984621 |
0.02054538 |
0.2604292 |
| cnvi0111204 |
NC |
0 |
0.9877504 |
1.297123 |
0.9992982 |
0.0903394 |
Total number of rows: 299140
Table truncated, full table size 17115 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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