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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_100 |
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
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Extracted molecule |
genomic DNA |
Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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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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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
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Department |
Health Studies
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Street address |
900 E 57th Street
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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 |
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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 |
0.9792382 |
1.416793 |
1 |
-0.03678534 |
cnvi0111186 |
NC |
0 |
0.01527756 |
0.5355757 |
0 |
0.1049259 |
cnvi0111187 |
NC |
0 |
0.9888043 |
1.53094 |
1 |
0.002801618 |
cnvi0111188 |
NC |
0 |
0.007618307 |
1.282242 |
0 |
-0.02539547 |
cnvi0111189 |
NC |
0 |
0.02406869 |
1.429798 |
0 |
-0.0124998 |
cnvi0111190 |
NC |
0 |
0 |
0.5142928 |
0 |
0.5194601 |
cnvi0111191 |
NC |
0 |
0.01999907 |
0.89088 |
0 |
-0.3035282 |
cnvi0111192 |
NC |
0 |
0.01681796 |
1.167953 |
0 |
0.06832276 |
cnvi0111193 |
NC |
0 |
0.004700164 |
1.205609 |
0 |
-0.01006203 |
cnvi0111194 |
NC |
0 |
0.9870797 |
1.186222 |
1 |
-0.165821 |
cnvi0111195 |
NC |
0 |
0.02907448 |
2.09256 |
0 |
0.0998771 |
cnvi0111196 |
NC |
0 |
0.9873608 |
1.180499 |
1 |
-0.05631332 |
cnvi0111197 |
NC |
0 |
0.003975812 |
1.120359 |
0 |
0.3277555 |
cnvi0111198 |
NC |
0 |
0.9696441 |
1.111436 |
0.9990836 |
-0.222797 |
cnvi0111199 |
NC |
0 |
0.01051419 |
1.454742 |
0 |
0.1942041 |
cnvi0111200 |
NC |
0 |
0.9907858 |
0.9331083 |
1 |
0.08131112 |
cnvi0111201 |
NC |
0 |
0.01648602 |
0.8590913 |
0 |
-0.1065066 |
cnvi0111202 |
NC |
0 |
0.9371418 |
1.362478 |
1 |
0.03134183 |
cnvi0111203 |
NC |
0 |
0.04922658 |
1.932642 |
0.0255357 |
0.2221401 |
cnvi0111204 |
NC |
0 |
0.9920493 |
1.19006 |
1 |
-0.03394195 |
Total number of rows: 299140
Table truncated, full table size 17107 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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