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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_81 |
| 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
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Gentra Puregene kit standard protocol.
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| 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
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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 |
|
| 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 |
0.9836577 |
1.293329 |
1 |
-0.168325 |
| cnvi0111186 |
NC |
0 |
0.01031484 |
0.5498885 |
0 |
0.1429745 |
| cnvi0111187 |
NC |
0 |
0.9860875 |
1.304219 |
1 |
-0.2284297 |
| cnvi0111188 |
NC |
0 |
0.01566098 |
1.21132 |
0.000953724 |
-0.107485 |
| cnvi0111189 |
NC |
0 |
0.0297371 |
1.358112 |
0.003572824 |
-0.08670858 |
| cnvi0111190 |
NC |
0 |
0 |
0.4460086 |
0 |
0.3139416 |
| cnvi0111191 |
NC |
0 |
0.02993797 |
0.4175544 |
0.001351108 |
-1.396795 |
| cnvi0111192 |
NC |
0 |
0.02011391 |
1.058161 |
0 |
-0.07409951 |
| cnvi0111193 |
NC |
0 |
0.007339679 |
1.17915 |
0 |
-0.04207626 |
| cnvi0111194 |
NC |
0 |
0.9889066 |
1.252713 |
1 |
-0.08713841 |
| cnvi0111195 |
NC |
0 |
0.02757182 |
2.189367 |
0 |
0.1651221 |
| cnvi0111196 |
NC |
0 |
0.9837365 |
1.074435 |
1 |
-0.192132 |
| cnvi0111197 |
NC |
0 |
0.009894647 |
0.966733 |
0 |
0.1149843 |
| cnvi0111198 |
NC |
0 |
0.9714187 |
1.232356 |
1 |
-0.07380259 |
| cnvi0111199 |
NC |
0 |
0.008570444 |
1.278744 |
0 |
0.008168673 |
| cnvi0111200 |
NC |
0 |
0.993578 |
0.9313239 |
1 |
0.07854971 |
| cnvi0111201 |
NC |
0 |
0.02564294 |
0.8849197 |
0.00751482 |
-0.06377147 |
| cnvi0111202 |
NC |
0 |
0.9487869 |
1.30476 |
1 |
-0.03110657 |
| cnvi0111203 |
NC |
0 |
0.04525676 |
1.904665 |
0.0213599 |
0.2011024 |
| cnvi0111204 |
NC |
0 |
0.9954491 |
1.41774 |
1 |
0.2186174 |
Total number of rows: 299140
Table truncated, full table size 17173 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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