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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_121 |
Sample type |
genomic |
|
|
Source name |
Colon tissue, normal
|
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
|
Organization name |
The University of Chicago
|
Department |
Health Studies
|
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 |
0.9784834 |
1.366583 |
1 |
-0.08884112 |
cnvi0111186 |
NC |
0 |
0.002425399 |
0.5987678 |
0 |
0.265832 |
cnvi0111187 |
NC |
0 |
0.986214 |
1.570905 |
1 |
0.03997995 |
cnvi0111188 |
NC |
0 |
0.009548927 |
1.276793 |
0 |
-0.03153959 |
cnvi0111189 |
NC |
0 |
0.02327095 |
1.54513 |
0 |
0.09941677 |
cnvi0111190 |
NC |
0 |
0 |
0.5183487 |
0 |
0.5307931 |
cnvi0111191 |
NC |
0 |
0.02305101 |
1.106352 |
0 |
0.00897933 |
cnvi0111192 |
NC |
0 |
0.01867829 |
1.129059 |
0 |
0.01946226 |
cnvi0111193 |
NC |
0 |
0.005782187 |
1.209384 |
0 |
-0.005551583 |
cnvi0111194 |
NC |
0 |
0.9881461 |
1.305056 |
1 |
-0.02808315 |
cnvi0111195 |
NC |
0 |
0.02989645 |
2.015672 |
0 |
0.04586945 |
cnvi0111196 |
NC |
0 |
0.9884201 |
1.232648 |
1 |
0.006050943 |
cnvi0111197 |
NC |
0 |
0.005136089 |
1.065076 |
0 |
0.2547515 |
cnvi0111198 |
NC |
0 |
0.9763807 |
1.22342 |
1 |
-0.08430266 |
cnvi0111199 |
NC |
0 |
0.009893738 |
1.506216 |
0 |
0.2443694 |
cnvi0111200 |
NC |
0 |
0.9872952 |
1.018263 |
1 |
0.2073044 |
cnvi0111201 |
NC |
0 |
0.007576468 |
0.8719272 |
0 |
-0.08511034 |
cnvi0111202 |
NC |
0 |
0.9380322 |
1.451051 |
1 |
0.1222079 |
cnvi0111203 |
NC |
0 |
0.05009267 |
1.914648 |
0.02644673 |
0.2086444 |
cnvi0111204 |
NC |
0 |
0.9882301 |
1.153134 |
0.9997959 |
-0.0794157 |
Total number of rows: 299140
Table truncated, full table size 17121 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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