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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_116 |
Sample type |
genomic |
|
|
Source name |
Colon tissue, normal
|
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.
|
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
|
Organization name |
The University of Chicago
|
Department |
Health Studies
|
Street address |
900 E 57th Street
|
City |
Chicago |
ZIP/Postal code |
60637 |
Country |
USA |
|
|
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 |
0.9762012 |
1.1383 |
1 |
-0.3525331 |
cnvi0111186 |
NC |
0 |
0.008918325 |
0.6074384 |
0 |
0.2865735 |
cnvi0111187 |
NC |
0 |
0.9885722 |
1.594398 |
1 |
0.06139542 |
cnvi0111188 |
NC |
0 |
0.01268756 |
1.266984 |
0 |
-0.04266676 |
cnvi0111189 |
NC |
0 |
0.02449895 |
1.436565 |
0 |
-0.005687469 |
cnvi0111190 |
NC |
0 |
0 |
0.4293394 |
0 |
0.2589887 |
cnvi0111191 |
NC |
0 |
0.02445461 |
0.6505828 |
0 |
-0.7570266 |
cnvi0111192 |
NC |
0 |
0.02209582 |
1.154422 |
0 |
0.05151203 |
cnvi0111193 |
NC |
0 |
0.003442586 |
1.28213 |
0 |
0.07871822 |
cnvi0111194 |
NC |
0 |
0.9939502 |
1.375602 |
1 |
0.04786892 |
cnvi0111195 |
NC |
0 |
0.03350077 |
1.915049 |
0.001003391 |
-0.02800996 |
cnvi0111196 |
NC |
0 |
0.9857907 |
1.083718 |
1 |
-0.1797206 |
cnvi0111197 |
NC |
0 |
0.005667403 |
0.9240519 |
0 |
0.04984068 |
cnvi0111198 |
NC |
0 |
0.9732426 |
1.320548 |
1 |
0.02591504 |
cnvi0111199 |
NC |
0 |
0.01430173 |
1.435399 |
0 |
0.1748923 |
cnvi0111200 |
NC |
0 |
0.9894928 |
0.8675397 |
1 |
-0.02380358 |
cnvi0111201 |
NC |
0 |
0.02210052 |
0.8002673 |
0.003813273 |
-0.208836 |
cnvi0111202 |
NC |
0 |
0.94132 |
1.426952 |
1 |
0.0980463 |
cnvi0111203 |
NC |
0 |
0.04042035 |
1.706711 |
0.01627255 |
0.04278426 |
cnvi0111204 |
NC |
0 |
0.9889184 |
1.446677 |
1 |
0.2477671 |
Total number of rows: 299140
Table truncated, full table size 17163 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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