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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_69 |
| 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
|
| 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
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| 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 |
0.9782272 |
1.29548 |
1 |
-0.1659274 |
| cnvi0111186 |
NC |
0 |
0.006931229 |
0.5158364 |
0 |
0.05074908 |
| cnvi0111187 |
NC |
0 |
0.9904152 |
1.578837 |
1 |
0.04724565 |
| cnvi0111188 |
NC |
0 |
0.01035943 |
1.30057 |
0 |
-0.004920049 |
| cnvi0111189 |
NC |
0 |
0.02578104 |
1.607299 |
0 |
0.1563271 |
| cnvi0111190 |
NC |
0 |
0 |
0.5607795 |
0 |
0.6443037 |
| cnvi0111191 |
NC |
0 |
0.03974577 |
0.2749895 |
0.01170718 |
-1.999383 |
| cnvi0111192 |
NC |
0 |
0.02522431 |
1.227038 |
0 |
0.1395206 |
| cnvi0111193 |
NC |
0 |
0.005452881 |
1.165819 |
0 |
-0.05847991 |
| cnvi0111194 |
NC |
0 |
0.9874168 |
1.249889 |
1 |
-0.09039457 |
| cnvi0111195 |
NC |
0 |
0.03614016 |
2.232758 |
0.003801547 |
0.1934353 |
| cnvi0111196 |
NC |
0 |
0.9862805 |
1.19066 |
1 |
-0.04394815 |
| cnvi0111197 |
NC |
0 |
0.004832904 |
0.9587003 |
0 |
0.1029466 |
| cnvi0111198 |
NC |
0 |
0.9610904 |
1.23111 |
0.9900441 |
-0.07526183 |
| cnvi0111199 |
NC |
0 |
0.008561457 |
1.469035 |
0 |
0.2083095 |
| cnvi0111200 |
NC |
0 |
0.9876083 |
0.8932228 |
1 |
0.01828672 |
| cnvi0111201 |
NC |
0 |
0.02532592 |
0.8303668 |
0.007183569 |
-0.1555692 |
| cnvi0111202 |
NC |
0 |
0.9337826 |
1.362893 |
1 |
0.03178141 |
| cnvi0111203 |
NC |
0 |
0.04870367 |
2.004408 |
0.02498565 |
0.2747414 |
| cnvi0111204 |
NC |
0 |
0.9916627 |
1.131082 |
1 |
-0.1072723 |
Total number of rows: 299140
Table truncated, full table size 17192 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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