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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_71 |
| Sample type |
genomic |
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| Source name |
Colon tissue, tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal cancer (CRC)
tissue: colon tumor
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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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| 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
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| 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 |
0.9828465 |
1.326044 |
1 |
-0.1322853 |
| cnvi0111186 |
NC |
0 |
0.005849743 |
0.4421745 |
0 |
-0.1715487 |
| cnvi0111187 |
NC |
0 |
0.9865416 |
1.429311 |
1 |
-0.0962965 |
| cnvi0111188 |
NC |
0 |
0.01080373 |
1.286041 |
0 |
-0.02112745 |
| cnvi0111189 |
NC |
0 |
0.02109986 |
1.639794 |
0 |
0.1852039 |
| cnvi0111190 |
NC |
0 |
0.005812152 |
0.4497572 |
0 |
0.3260168 |
| cnvi0111191 |
NC |
0 |
0.02101942 |
1.338156 |
0 |
0.2834149 |
| cnvi0111192 |
NC |
0 |
0.01390213 |
1.184692 |
0 |
0.08885317 |
| cnvi0111193 |
NC |
0 |
0.002998088 |
1.123477 |
0 |
-0.1118535 |
| cnvi0111194 |
NC |
0 |
0.9936643 |
1.255858 |
1 |
-0.08352143 |
| cnvi0111195 |
NC |
0 |
0.02559032 |
2.357206 |
0 |
0.2716865 |
| cnvi0111196 |
NC |
0 |
0.9900455 |
1.275307 |
1 |
0.05513442 |
| cnvi0111197 |
NC |
0 |
0.007501154 |
0.9897075 |
0 |
0.1488689 |
| cnvi0111198 |
NC |
0 |
0.9713362 |
1.145223 |
1 |
-0.1795938 |
| cnvi0111199 |
NC |
0 |
0.009283818 |
1.627559 |
0 |
0.3561505 |
| cnvi0111200 |
NC |
0 |
0.9904034 |
0.9551468 |
1 |
0.1149892 |
| cnvi0111201 |
NC |
0 |
0.01273422 |
0.8411956 |
0 |
-0.1368767 |
| cnvi0111202 |
NC |
0 |
0.9359715 |
1.425059 |
1 |
0.09613074 |
| cnvi0111203 |
NC |
0 |
0.03550324 |
2.134584 |
0.01110031 |
0.3655203 |
| cnvi0111204 |
NC |
0 |
0.9895064 |
1.246702 |
1 |
0.03314117 |
Total number of rows: 299140
Table truncated, full table size 16974 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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