|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_62 |
Sample type |
genomic |
|
|
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.
|
|
|
Hybridization protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.
|
Scan protocol |
Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using the Illumina BeadArray scanner.
|
Data processing |
Illumina BeadStudio v3.3.4 normalized intensity values and BAF data were imported into PARTEK Genomics Suite for statistical analysis.
|
|
|
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 |
|
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 |
0.97618 |
1.451332 |
1 |
-0.00203676 |
cnvi0111186 |
NC |
0 |
0.01626105 |
0.4984345 |
0 |
0.001239419 |
cnvi0111187 |
NC |
0 |
0.9836282 |
1.48454 |
0.9984189 |
-0.04160034 |
cnvi0111188 |
NC |
0 |
0.01267008 |
1.251328 |
0 |
-0.06060397 |
cnvi0111189 |
NC |
0 |
0.02445299 |
1.338435 |
0 |
-0.1077635 |
cnvi0111190 |
NC |
0 |
0.00246899 |
0.4994291 |
0 |
0.4771501 |
cnvi0111191 |
NC |
0 |
0.03271637 |
0.7210831 |
0.00428482 |
-0.6085938 |
cnvi0111192 |
NC |
0 |
0.01775885 |
1.076488 |
0 |
-0.04932627 |
cnvi0111193 |
NC |
0 |
0.00798492 |
1.236599 |
0 |
0.02655405 |
cnvi0111194 |
NC |
0 |
0.9845182 |
1.270462 |
1 |
-0.06684158 |
cnvi0111195 |
NC |
0 |
0.03499437 |
2.192851 |
0.002586832 |
0.1674162 |
cnvi0111196 |
NC |
0 |
0.9891295 |
1.162957 |
1 |
-0.07791298 |
cnvi0111197 |
NC |
0 |
0.01127622 |
0.9518107 |
0 |
0.09254135 |
cnvi0111198 |
NC |
0 |
0.9643682 |
1.24237 |
0.993508 |
-0.06212643 |
cnvi0111199 |
NC |
0 |
0.00832659 |
1.415003 |
0 |
0.1542457 |
cnvi0111200 |
NC |
0 |
0.9929538 |
0.8429611 |
1 |
-0.06526726 |
cnvi0111201 |
NC |
0 |
0.02422213 |
0.7855636 |
0.006030191 |
-0.2355898 |
cnvi0111202 |
NC |
0 |
0.9401807 |
1.380598 |
1 |
0.05040237 |
cnvi0111203 |
NC |
0 |
0.0258889 |
1.480051 |
0.0009871102 |
-0.1627873 |
cnvi0111204 |
NC |
0 |
0.985382 |
1.075631 |
0.9968406 |
-0.1797918 |
Total number of rows: 299140
Table truncated, full table size 17211 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
|
|
|
|
|