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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_99 |
Sample type |
genomic |
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|
Source name |
Colon tissue, tumor
|
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
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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
|
Organization name |
The University of Chicago
|
Department |
Health Studies
|
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 |
0.9789044 |
1.273082 |
1 |
-0.191089 |
cnvi0111186 |
NC |
0 |
0.009138515 |
0.5045285 |
0 |
0.01877111 |
cnvi0111187 |
NC |
0 |
0.9857877 |
1.408934 |
1 |
-0.1170122 |
cnvi0111188 |
NC |
0 |
0.009155501 |
1.171451 |
0 |
-0.1557675 |
cnvi0111189 |
NC |
0 |
0.02485193 |
1.495714 |
0 |
0.05252315 |
cnvi0111190 |
NC |
0 |
0.007588857 |
0.5265248 |
0 |
0.5533717 |
cnvi0111191 |
NC |
0 |
0.02578684 |
1.255044 |
0 |
0.1909063 |
cnvi0111192 |
NC |
0 |
0.01474079 |
1.119737 |
0 |
0.007501085 |
cnvi0111193 |
NC |
0 |
0.007731297 |
1.15099 |
0 |
-0.07694848 |
cnvi0111194 |
NC |
0 |
0.991454 |
1.181819 |
1 |
-0.1711858 |
cnvi0111195 |
NC |
0 |
0.03027926 |
2.04548 |
0 |
0.06704751 |
cnvi0111196 |
NC |
0 |
0.9865288 |
1.210907 |
1 |
-0.0196219 |
cnvi0111197 |
NC |
0 |
0.006512857 |
0.9546294 |
0 |
0.09680754 |
cnvi0111198 |
NC |
0 |
0.9743506 |
1.062373 |
1 |
-0.2879319 |
cnvi0111199 |
NC |
0 |
0.01510499 |
1.325975 |
0 |
0.06049471 |
cnvi0111200 |
NC |
0 |
0.9838306 |
0.9306415 |
0.9996276 |
0.07749221 |
cnvi0111201 |
NC |
0 |
0.01661989 |
0.8682036 |
0 |
-0.09128455 |
cnvi0111202 |
NC |
0 |
0.9230651 |
1.304159 |
0.997166 |
-0.03177053 |
cnvi0111203 |
NC |
0 |
0.04632569 |
1.802473 |
0.02248429 |
0.1215429 |
cnvi0111204 |
NC |
0 |
0.990629 |
1.173389 |
1 |
-0.05429395 |
Total number of rows: 299140
Table truncated, full table size 17238 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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