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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_85 |
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 |
0.9798672 |
1.519791 |
1 |
0.06445841 |
cnvi0111186 |
NC |
0 |
0.0053099 |
0.5608318 |
0 |
0.1714036 |
cnvi0111187 |
NC |
0 |
0.983291 |
1.542553 |
0.9980679 |
0.0137035 |
cnvi0111188 |
NC |
0 |
0.01211363 |
1.352388 |
0 |
0.05144425 |
cnvi0111189 |
NC |
0 |
0.02075354 |
1.437493 |
0 |
-0.004755765 |
cnvi0111190 |
NC |
0 |
0.003190284 |
0.506598 |
0 |
0.4977116 |
cnvi0111191 |
NC |
0 |
0.04837665 |
0.320885 |
0.02082053 |
-1.776703 |
cnvi0111192 |
NC |
0 |
0.01646189 |
1.149049 |
0 |
0.0447809 |
cnvi0111193 |
NC |
0 |
0.003266854 |
1.239209 |
0 |
0.02959565 |
cnvi0111194 |
NC |
0 |
0.9902782 |
1.212286 |
1 |
-0.1344643 |
cnvi0111195 |
NC |
0 |
0.02943577 |
2.245957 |
0 |
0.201939 |
cnvi0111196 |
NC |
0 |
0.9899023 |
1.185499 |
1 |
-0.05021613 |
cnvi0111197 |
NC |
0 |
0.007827044 |
1.043846 |
0 |
0.2257044 |
cnvi0111198 |
NC |
0 |
0.9859843 |
1.310087 |
1 |
0.01444108 |
cnvi0111199 |
NC |
0 |
0.006208393 |
1.471381 |
0 |
0.2106117 |
cnvi0111200 |
NC |
0 |
0.9928895 |
0.9329199 |
1 |
0.08101988 |
cnvi0111201 |
NC |
0 |
0.01845942 |
0.8836632 |
8.618292E-06 |
-0.06582136 |
cnvi0111202 |
NC |
0 |
0.9478654 |
1.488231 |
1 |
0.1587077 |
cnvi0111203 |
NC |
0 |
0.04153019 |
1.969399 |
0.01743997 |
0.2493208 |
cnvi0111204 |
NC |
0 |
0.9907256 |
1.298112 |
1 |
0.09143906 |
Total number of rows: 299140
Table truncated, full table size 17127 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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