|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Dec 19, 2014 |
Title |
Colon Tissue Sample_131 |
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.
|
|
|
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 |
0.9712114 |
1.457796 |
0.9961801 |
0.004374865 |
cnvi0111186 |
NC |
0 |
0.02296923 |
0.5900903 |
0 |
0.2447713 |
cnvi0111187 |
NC |
0 |
0.9810752 |
1.497421 |
0.9957609 |
-0.02913614 |
cnvi0111188 |
NC |
0 |
0.01220785 |
1.248437 |
0 |
-0.06394171 |
cnvi0111189 |
NC |
0 |
0.02445984 |
1.40038 |
0 |
-0.04249301 |
cnvi0111190 |
NC |
0 |
0.007576612 |
0.6440983 |
0 |
0.8441511 |
cnvi0111191 |
NC |
0 |
0.04078175 |
1.283233 |
0.01280107 |
0.2229515 |
cnvi0111192 |
NC |
0 |
0.02315383 |
1.127975 |
0 |
0.01807544 |
cnvi0111193 |
NC |
0 |
0.009053124 |
1.246029 |
0 |
0.03751428 |
cnvi0111194 |
NC |
0 |
0.9878858 |
1.147611 |
1 |
-0.2135611 |
cnvi0111195 |
NC |
0 |
0.04178092 |
2.012782 |
0.009781623 |
0.0437994 |
cnvi0111196 |
NC |
0 |
0.9841318 |
1.01979 |
1 |
-0.2674379 |
cnvi0111197 |
NC |
0 |
0.01010527 |
0.9734105 |
0 |
0.1249151 |
cnvi0111198 |
NC |
0 |
0.9644699 |
1.27392 |
0.9936155 |
-0.02594674 |
cnvi0111199 |
NC |
0 |
0.01158565 |
1.455116 |
0 |
0.1945747 |
cnvi0111200 |
NC |
0 |
0.9946304 |
0.9134021 |
1 |
0.05051671 |
cnvi0111201 |
NC |
0 |
0.030041 |
0.7761384 |
0.01211045 |
-0.253004 |
cnvi0111202 |
NC |
0 |
0.9330857 |
1.321491 |
1 |
-0.01272414 |
cnvi0111203 |
NC |
0 |
0.04654821 |
1.907495 |
0.02271835 |
0.2032445 |
cnvi0111204 |
NC |
0 |
0.9889826 |
1.10707 |
1 |
-0.1382287 |
Total number of rows: 299140
Table truncated, full table size 17501 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
|
|
|
|
|