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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_113 |
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 |
0.9800331 |
1.376408 |
1 |
-0.07850628 |
cnvi0111186 |
NC |
0 |
0.007813486 |
0.5573166 |
0 |
0.1623326 |
cnvi0111187 |
NC |
0 |
0.9835317 |
1.433427 |
0.9983184 |
-0.09214799 |
cnvi0111188 |
NC |
0 |
0.007940056 |
1.347788 |
0 |
0.04652905 |
cnvi0111189 |
NC |
0 |
0.02105149 |
1.528271 |
0 |
0.08358944 |
cnvi0111190 |
NC |
0 |
0 |
0.3966437 |
0 |
0.144714 |
cnvi0111191 |
NC |
0 |
0.02181158 |
1.176513 |
0 |
0.09768654 |
cnvi0111192 |
NC |
0 |
0.01139653 |
1.1393 |
0 |
0.0324891 |
cnvi0111193 |
NC |
0 |
0.005216482 |
1.281443 |
0 |
0.0779459 |
cnvi0111194 |
NC |
0 |
0.9822894 |
1.127078 |
0.9993607 |
-0.2396076 |
cnvi0111195 |
NC |
0 |
0.02369434 |
2.183862 |
0 |
0.1614899 |
cnvi0111196 |
NC |
0 |
0.9839943 |
1.185594 |
1 |
-0.05010051 |
cnvi0111197 |
NC |
0 |
0.006924808 |
0.9237431 |
0 |
0.04935847 |
cnvi0111198 |
NC |
0 |
0.9807165 |
1.218851 |
1 |
-0.08970058 |
cnvi0111199 |
NC |
0 |
0.009509334 |
1.502292 |
0 |
0.2406059 |
cnvi0111200 |
NC |
0 |
0.9958292 |
1.021811 |
1 |
0.2123238 |
cnvi0111201 |
NC |
0 |
0.01779235 |
0.8236012 |
0 |
-0.167372 |
cnvi0111202 |
NC |
0 |
0.9519231 |
1.526242 |
1 |
0.1950927 |
cnvi0111203 |
NC |
0 |
0.03859301 |
1.947571 |
0.01435039 |
0.2332415 |
cnvi0111204 |
NC |
0 |
0.9925668 |
0.9297673 |
1 |
-0.3900341 |
Total number of rows: 299140
Table truncated, full table size 16976 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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