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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_103 |
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
|
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 |
|
|
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 |
0.9741281 |
1.55967 |
0.9992488 |
0.101827 |
cnvi0111186 |
NC |
0 |
0.01752798 |
0.5530285 |
0 |
0.1511892 |
cnvi0111187 |
NC |
0 |
0.9862377 |
1.445286 |
1 |
-0.0802616 |
cnvi0111188 |
NC |
0 |
0.006732557 |
1.266772 |
0 |
-0.04290799 |
cnvi0111189 |
NC |
0 |
0.02155343 |
1.663992 |
0 |
0.2063378 |
cnvi0111190 |
NC |
0 |
0 |
0.4967291 |
0 |
0.4693295 |
cnvi0111191 |
NC |
0 |
0.02665928 |
1.050726 |
0 |
-0.06544501 |
cnvi0111192 |
NC |
0 |
0.01942926 |
1.165331 |
0 |
0.06508063 |
cnvi0111193 |
NC |
0 |
0.003571041 |
1.168732 |
0 |
-0.05487944 |
cnvi0111194 |
NC |
0 |
0.9862122 |
1.312907 |
1 |
-0.01943026 |
cnvi0111195 |
NC |
0 |
0.03415387 |
2.015536 |
0.001695781 |
0.04577184 |
cnvi0111196 |
NC |
0 |
0.9886773 |
1.231189 |
1 |
0.004342172 |
cnvi0111197 |
NC |
0 |
0.001831047 |
1.049974 |
0 |
0.2341482 |
cnvi0111198 |
NC |
0 |
0.9702238 |
1.237131 |
0.9996963 |
-0.06822418 |
cnvi0111199 |
NC |
0 |
0.0104407 |
1.290288 |
0 |
0.02113391 |
cnvi0111200 |
NC |
0 |
0.9869694 |
0.9518876 |
1 |
0.1100579 |
cnvi0111201 |
NC |
0 |
0.01493238 |
0.8482124 |
0 |
-0.1248925 |
cnvi0111202 |
NC |
0 |
0.9334325 |
1.498659 |
1 |
0.1687815 |
cnvi0111203 |
NC |
0 |
0.04677056 |
2.034177 |
0.02295224 |
0.2960107 |
cnvi0111204 |
NC |
0 |
0.9899651 |
1.29061 |
1 |
0.08307708 |
Total number of rows: 299140
Table truncated, full table size 17124 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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