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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_74 |
| 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 |
0.9778417 |
1.265627 |
1 |
-0.1995624 |
| cnvi0111186 |
NC |
0 |
0.02605525 |
0.2392899 |
0 |
-1.057405 |
| cnvi0111187 |
NC |
0 |
0.9945298 |
1.595914 |
1 |
0.06276695 |
| cnvi0111188 |
NC |
0 |
0.008254992 |
1.32662 |
0 |
0.02369039 |
| cnvi0111189 |
NC |
0 |
0.02538416 |
1.44113 |
0 |
-0.001110855 |
| cnvi0111190 |
NC |
0 |
0.002289656 |
0.5767683 |
0 |
0.684862 |
| cnvi0111191 |
NC |
0 |
0.02923984 |
0.7228169 |
0.0006139449 |
-0.605129 |
| cnvi0111192 |
NC |
0 |
0.01854961 |
1.464012 |
0 |
0.3942686 |
| cnvi0111193 |
NC |
0 |
0.01065675 |
0.3163723 |
0 |
-1.940129 |
| cnvi0111194 |
NC |
0 |
0.9841897 |
1.679582 |
1 |
0.3359074 |
| cnvi0111195 |
NC |
0 |
0.03749269 |
2.368996 |
0.005235441 |
0.278884 |
| cnvi0111196 |
NC |
0 |
0.9928309 |
1.208723 |
1 |
-0.02222648 |
| cnvi0111197 |
NC |
0 |
0.008487081 |
1.051321 |
0 |
0.2359984 |
| cnvi0111198 |
NC |
0 |
0.9683134 |
1.115329 |
0.9976773 |
-0.2177522 |
| cnvi0111199 |
NC |
0 |
0.01431181 |
2.021711 |
0 |
0.6690176 |
| cnvi0111200 |
NC |
0 |
0.9877374 |
0.8941146 |
1 |
0.01972641 |
| cnvi0111201 |
NC |
0 |
0.02382008 |
0.728311 |
0.005610084 |
-0.3447634 |
| cnvi0111202 |
NC |
0 |
0.9427249 |
1.688251 |
1 |
0.3406383 |
| cnvi0111203 |
NC |
0 |
0.03115342 |
0.8529814 |
0.006524784 |
-0.9578483 |
| cnvi0111204 |
NC |
0 |
0.9965392 |
1.559383 |
1 |
0.3559999 |
Total number of rows: 299140
Table truncated, full table size 17093 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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