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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_64 |
| 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.
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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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| 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 |
0.9740912 |
1.419088 |
0.9992099 |
-0.03445037 |
| cnvi0111186 |
NC |
0 |
0.007814005 |
0.5751681 |
0 |
0.2078192 |
| cnvi0111187 |
NC |
0 |
0.9858304 |
1.486257 |
1 |
-0.03993272 |
| cnvi0111188 |
NC |
0 |
0.01080262 |
1.315671 |
0 |
0.01173383 |
| cnvi0111189 |
NC |
0 |
0.02898691 |
1.552448 |
0.002782576 |
0.106234 |
| cnvi0111190 |
NC |
0 |
0.004830999 |
0.5605369 |
0 |
0.6436796 |
| cnvi0111191 |
NC |
0 |
0.04977916 |
0.3809106 |
0.02230145 |
-1.529307 |
| cnvi0111192 |
NC |
0 |
0.02388489 |
1.202216 |
0 |
0.1100367 |
| cnvi0111193 |
NC |
0 |
0.008173076 |
1.152283 |
0 |
-0.07532936 |
| cnvi0111194 |
NC |
0 |
0.983641 |
1.253991 |
1 |
-0.08566784 |
| cnvi0111195 |
NC |
0 |
0.0404076 |
2.354297 |
0.008325692 |
0.269905 |
| cnvi0111196 |
NC |
0 |
0.9869131 |
1.14521 |
1 |
-0.1000977 |
| cnvi0111197 |
NC |
0 |
0.01082346 |
1.023628 |
0 |
0.197487 |
| cnvi0111198 |
NC |
0 |
0.9686573 |
1.268345 |
0.9980407 |
-0.03227508 |
| cnvi0111199 |
NC |
0 |
0.007887685 |
1.373356 |
0 |
0.1111467 |
| cnvi0111200 |
NC |
0 |
0.9895697 |
0.8513258 |
1 |
-0.0510221 |
| cnvi0111201 |
NC |
0 |
0.0241705 |
0.8656834 |
0.005976244 |
-0.09547847 |
| cnvi0111202 |
NC |
0 |
0.943092 |
1.42009 |
1 |
0.09109133 |
| cnvi0111203 |
NC |
0 |
0.04511311 |
1.939845 |
0.02120879 |
0.2275068 |
| cnvi0111204 |
NC |
0 |
0.9846214 |
1.117083 |
0.9960513 |
-0.1252394 |
Total number of rows: 299140
Table truncated, full table size 17354 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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