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Sample GSM853344 Query DataSets for GSM853344
Status Public on Dec 19, 2014
Title Colon Tissue Sample_80
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 0.9825213 1.379645 1 -0.07511662
cnvi0111186 NC 0 0.006718221 0.5401444 0 0.1171807
cnvi0111187 NC 0 0.9859345 1.452244 1 -0.07333261
cnvi0111188 NC 0 0.008195232 1.400666 0 0.1020488
cnvi0111189 NC 0 0.02249618 1.488479 0 0.04552786
cnvi0111190 NC 0 0 0.5050345 0 0.4932522
cnvi0111191 NC 0 0.02530498 1.086129 0 -0.0176357
cnvi0111192 NC 0 0.0150058 1.088725 0 -0.03301915
cnvi0111193 NC 0 0.006478692 1.277717 0 0.07374398
cnvi0111194 NC 0 0.9899362 1.235166 1 -0.1074902
cnvi0111195 NC 0 0.02966406 2.307171 0 0.2407331
cnvi0111196 NC 0 0.9862208 1.214942 1 -0.01482324
cnvi0111197 NC 0 0.002397085 0.8836604 0 -0.01464117
cnvi0111198 NC 0 0.9704284 1.259673 0.9999125 -0.04217235
cnvi0111199 NC 0 0.005700997 1.299718 0 0.03163987
cnvi0111200 NC 0 0.9938308 0.8513193 1 -0.05103301
cnvi0111201 NC 0 0.01809052 0.8299747 0 -0.1562507
cnvi0111202 NC 0 0.943075 1.264846 1 -0.07592877
cnvi0111203 NC 0 0.04240425 1.974045 0.01835938 0.2527205
cnvi0111204 NC 0 0.9914681 1.074358 1 -0.1815003

Total number of rows: 299140

Table truncated, full table size 17057 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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