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Sample GSM853244 Query DataSets for GSM853244
Status Public on Dec 19, 2014
Title Colon Tissue Sample_104
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 0.9801014 1.401016 1 -0.05294114
cnvi0111186 NC 0 0 0.5262768 0 0.07965732
cnvi0111187 NC 0 0.9872446 1.595245 1 0.06216205
cnvi0111188 NC 0 0.005825108 1.38007 0 0.08067728
cnvi0111189 NC 0 0.0226669 1.580667 0 0.1322229
cnvi0111190 NC 0 0 0.3847545 0 0.1008085
cnvi0111191 NC 0 0.02614665 0.8264873 0 -0.4117667
cnvi0111192 NC 0 0.01516258 1.281123 0 0.2017495
cnvi0111193 NC 0 0.003714692 1.154612 0 -0.07241528
cnvi0111194 NC 0 0.9792073 1.125844 0.9961447 -0.2411882
cnvi0111195 NC 0 0.02629102 2.142069 0 0.1336134
cnvi0111196 NC 0 0.9886219 1.147401 1 -0.09734073
cnvi0111197 NC 0 0.002936021 1.076403 0 0.2700135
cnvi0111198 NC 0 0.9656379 1.181124 0.9948499 -0.1350614
cnvi0111199 NC 0 0.008889091 1.380732 0 0.1188742
cnvi0111200 NC 0 0.9886848 0.9075615 1 0.04126201
cnvi0111201 NC 0 0.01860251 0.8061505 0.0001581324 -0.1982688
cnvi0111202 NC 0 0.9354873 1.403772 1 0.07441764
cnvi0111203 NC 0 0.0372111 1.98375 0.01289678 0.2597953
cnvi0111204 NC 0 0.9933947 1.22177 1 0.00399735

Total number of rows: 299140

Table truncated, full table size 17004 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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