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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_149 |
| 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
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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 |
0.9791256 |
1.237784 |
1 |
-0.2316546 |
| cnvi0111186 |
NC |
0 |
0.0184513 |
0.4121428 |
0 |
-0.2730203 |
| cnvi0111187 |
NC |
0 |
0.9831398 |
1.549783 |
0.9979104 |
0.02045015 |
| cnvi0111188 |
NC |
0 |
0.008994014 |
1.196239 |
0 |
-0.1255589 |
| cnvi0111189 |
NC |
0 |
0.02282747 |
1.54415 |
0 |
0.09850221 |
| cnvi0111190 |
NC |
0 |
0 |
0.499958 |
0 |
0.4786772 |
| cnvi0111191 |
NC |
0 |
0.02866799 |
0.900565 |
1.01328E-05 |
-0.2879289 |
| cnvi0111192 |
NC |
0 |
0.01876707 |
1.163454 |
0 |
0.06275462 |
| cnvi0111193 |
NC |
0 |
0.005961393 |
1.151818 |
0 |
-0.07591097 |
| cnvi0111194 |
NC |
0 |
0.9864171 |
1.299253 |
1 |
-0.0345118 |
| cnvi0111195 |
NC |
0 |
0.03375074 |
2.064142 |
0.001268391 |
0.08015095 |
| cnvi0111196 |
NC |
0 |
0.9866694 |
1.140435 |
1 |
-0.1061254 |
| cnvi0111197 |
NC |
0 |
0.01145324 |
0.9719275 |
0 |
0.1227154 |
| cnvi0111198 |
NC |
0 |
0.9705908 |
1.085588 |
1 |
-0.2567448 |
| cnvi0111199 |
NC |
0 |
0.01535678 |
1.328926 |
0 |
0.06370168 |
| cnvi0111200 |
NC |
0 |
0.9932514 |
0.9375857 |
1 |
0.08821721 |
| cnvi0111201 |
NC |
0 |
0.02504278 |
0.6848636 |
0.006887709 |
-0.4335014 |
| cnvi0111202 |
NC |
0 |
0.95774 |
1.388337 |
1 |
0.05846695 |
| cnvi0111203 |
NC |
0 |
0.04400975 |
1.894006 |
0.02004818 |
0.1930061 |
| cnvi0111204 |
NC |
0 |
0.993378 |
1.169026 |
1 |
-0.05966897 |
Total number of rows: 299140
Table truncated, full table size 17128 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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