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Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_86 |
Sample type |
genomic |
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|
Source name |
Colon tissue, tumor
|
Organism |
Homo sapiens |
Characteristics |
disease state: colorectal cancer (CRC) tissue: colon tumor
|
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 |
|
|
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 |
0.9821166 |
1.330628 |
1 |
-0.1273065 |
cnvi0111186 |
NC |
0 |
0.008328877 |
0.4763979 |
0 |
-0.06399749 |
cnvi0111187 |
NC |
0 |
0.9846826 |
1.463818 |
0.9995166 |
-0.06188002 |
cnvi0111188 |
NC |
0 |
0.007719045 |
1.525662 |
0 |
0.2253705 |
cnvi0111189 |
NC |
0 |
0.0124693 |
1.669878 |
0 |
0.2114318 |
cnvi0111190 |
NC |
0 |
0.008673812 |
0.289832 |
0 |
-0.3079128 |
cnvi0111191 |
NC |
0 |
0.02787178 |
0.3238362 |
0 |
-1.763495 |
cnvi0111192 |
NC |
0 |
0.01227411 |
1.16447 |
0 |
0.06401439 |
cnvi0111193 |
NC |
0 |
0.003718058 |
1.230527 |
0 |
0.01945229 |
cnvi0111194 |
NC |
0 |
0.9866496 |
1.229303 |
1 |
-0.1143543 |
cnvi0111195 |
NC |
0 |
0.0205739 |
2.696167 |
0 |
0.4655184 |
cnvi0111196 |
NC |
0 |
0.9864097 |
1.169941 |
1 |
-0.06927451 |
cnvi0111197 |
NC |
0 |
0.005325417 |
0.9472783 |
0 |
0.08565511 |
cnvi0111198 |
NC |
0 |
0.9789993 |
1.295837 |
1 |
-0.001337456 |
cnvi0111199 |
NC |
0 |
0.00665368 |
1.600364 |
0 |
0.3318406 |
cnvi0111200 |
NC |
0 |
0.9982759 |
0.9069027 |
1 |
0.04021446 |
cnvi0111201 |
NC |
0 |
0.0117525 |
0.8428652 |
0 |
-0.1340162 |
cnvi0111202 |
NC |
0 |
0.9476968 |
1.37499 |
1 |
0.04453086 |
cnvi0111203 |
NC |
0 |
0.03518856 |
2.162983 |
0.0107693 |
0.3845879 |
cnvi0111204 |
NC |
0 |
0.9938653 |
1.277405 |
1 |
0.06823978 |
Total number of rows: 299140
Table truncated, full table size 16917 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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