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Sample GSM853318 Query DataSets for GSM853318
Status Public on Dec 19, 2014
Title Colon Tissue Sample_54
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 0.9787519 1.44253 1 -0.0108126
cnvi0111186 NC 0 0.01455266 0.6078941 0 0.2876554
cnvi0111187 NC 0 0.9854035 1.785595 1 0.2247884
cnvi0111188 NC 0 0.009137955 1.549713 0 0.2479368
cnvi0111189 NC 0 0.01862533 1.464227 0 0.02182817
cnvi0111190 NC 0 0 0.3885907 0 0.1151215
cnvi0111191 NC 0 0.025842 0.898109 0 -0.2918689
cnvi0111192 NC 0 0.01571012 1.169795 0 0.07059616
cnvi0111193 NC 0 0.008888146 1.218134 0 0.004849385
cnvi0111194 NC 0 0.9932736 1.314643 1 -0.01752347
cnvi0111195 NC 0 0.02689435 2.137784 0 0.1307247
cnvi0111196 NC 0 0.9878889 1.207681 1 -0.02347073
cnvi0111197 NC 0 0.01129202 0.9028651 0 0.01637721
cnvi0111198 NC 0 0.9797149 1.297845 1 0.0008966031
cnvi0111199 NC 0 0.0093338 1.541063 0 0.2773665
cnvi0111200 NC 0 0.9971942 0.8626364 1 -0.03198079
cnvi0111201 NC 0 0.01840931 0.9822171 0 0.08672388
cnvi0111202 NC 0 0.9419533 1.390188 1 0.06038886
cnvi0111203 NC 0 0.02654588 1.502735 0.001678183 -0.1408436
cnvi0111204 NC 0 0.9946514 1.318478 1 0.1138976

Total number of rows: 299140

Table truncated, full table size 17054 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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