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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_144 |
| Sample type |
genomic |
| |
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| Source name |
Colon tissue, normal
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| 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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| |
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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
|
| Department |
Health Studies
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| 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 |
0.9805574 |
1.364618 |
1 |
-0.09091698 |
| cnvi0111186 |
NC |
0 |
0.01623314 |
0.5411668 |
0 |
0.1199087 |
| cnvi0111187 |
NC |
0 |
0.9850854 |
1.609522 |
0.999936 |
0.07501556 |
| cnvi0111188 |
NC |
0 |
0.01234679 |
1.331527 |
0 |
0.02901756 |
| cnvi0111189 |
NC |
0 |
0.02752287 |
1.500208 |
0.001240363 |
0.056852 |
| cnvi0111190 |
NC |
0 |
0 |
0.52137 |
0 |
0.5391778 |
| cnvi0111191 |
NC |
0 |
0.04547374 |
0.4461811 |
0.01775535 |
-1.30113 |
| cnvi0111192 |
NC |
0 |
0.02308872 |
1.254544 |
0 |
0.1715036 |
| cnvi0111193 |
NC |
0 |
0.009198301 |
1.391153 |
0 |
0.1964568 |
| cnvi0111194 |
NC |
0 |
0.9812397 |
1.150163 |
0.9982654 |
-0.2103562 |
| cnvi0111195 |
NC |
0 |
0.03671442 |
2.136442 |
0.004410348 |
0.1298184 |
| cnvi0111196 |
NC |
0 |
0.9884473 |
1.164651 |
1 |
-0.07581248 |
| cnvi0111197 |
NC |
0 |
0.00629568 |
0.9625885 |
0 |
0.108786 |
| cnvi0111198 |
NC |
0 |
0.9705235 |
1.342397 |
1 |
0.04958935 |
| cnvi0111199 |
NC |
0 |
0.01127635 |
1.515836 |
0 |
0.253554 |
| cnvi0111200 |
NC |
0 |
0.9937766 |
0.9610319 |
1 |
0.1238509 |
| cnvi0111201 |
NC |
0 |
0.0213345 |
0.875478 |
0.003012842 |
-0.07924705 |
| cnvi0111202 |
NC |
0 |
0.9347646 |
1.308137 |
1 |
-0.02737665 |
| cnvi0111203 |
NC |
0 |
0.04509601 |
1.956702 |
0.02119081 |
0.2399895 |
| cnvi0111204 |
NC |
0 |
0.9878143 |
1.231052 |
0.9993644 |
0.01491618 |
Total number of rows: 299140
Table truncated, full table size 17370 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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