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Sample GSM849757 Query DataSets for GSM849757
Status Public on Dec 16, 2011
Title 340/USLAM
Sample type genomic
 
Source name Blood DNA
Organism Homo sapiens
Characteristics gender: male
age: 71
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood with QIAGEN kits
Label C-Bio and A-DNP
Label protocol 500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description Genomic DNA extracted from blood was genotyped using Infinium Human1MDuo Genotyping BeadChips (Illumina).
Data processing Genotypes and other intensity data were called and exported with Illumina GenomeStudio software
 
Submission date Dec 15, 2011
Last update date Dec 16, 2011
Contact name Devin Absher
E-mail(s) dabsher@hudsonalpha.org
Organization name HudsonAlpha Institute for Biotechnology
Street address 601 Genome Way
City Huntsville
State/province AL
ZIP/Postal code 35806
Country USA
 
Platform ID GPL6984
Series (1)
GSE34467 Somatic copy number variants in monozygotic twins and elderly single-born individuals

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB or NC (no call)
Score
Theta
R
B Allele Freq
Log R Ratio

Data table
ID_REF VALUE Score Theta R B Allele Freq Log R Ratio
rs12354060-128_T_F_1514243431 BB 0.3015375 0.9697844 1.737447 1 0.03228826
rs4345758-127_B_F_1516310071 AA 0.3136484 0.02537252 1.42031 0.00 -0.3493812
rs2691310-128_B_R_1514251078 NC 0.00 0.8175642 1.458771 0.717743 -0.06676301
rs2531266-128_T_R_1514250574 NC 0.00 0.9597466 1.541854 1 -0.3162448
rs4477212-128_B_R_1513978262 AA 0.3935362 0.04309363 0.4743624 0.005725965 -0.5995107
rs4124251-128_B_F_1514285504 NC 0.00 0.09598921 1.655942 0.008190486 0.06387281
rs1856862-127_T_F_1516310110 BB 0.4344913 0.9646899 0.5931199 0.9777814 -0.3943795
rs4096703-127_T_R_1516308906 AA 0.3580485 0.05647621 0.8441158 0.00 -0.1992551
rs8179466-128_B_F_1514290736 NC 0.00 0.8514559 1.586993 0.9703691 0.1120685
rs6603779-128_B_F_1514258763 NC 0.00 0.2305619 2.957925 0.3689908 -0.009860624
cnvi0007379-126_B_F_1514269226 NC 0.00 0.9150835 2.038895 1 -0.09655059
cnvi0019140-126_B_R_1525540355 NC 0.00 0.08013757 1.077016 0.00 -0.08113149
cnvi0007389-126_T_R_1514269233 NC 0.00 0.03449471 1.315534 0.00221802 0.01065632
cnvi0021559-126_T_F_1525544132 NC 0.00 0.07318167 4.149443 0.00 0.1189032
cnvi0007392-126_B_F_1514269234 NC 0.00 0.04449916 2.392374 0.00 0.3259743
cnvi0007380-126_B_F_1514269227 NC 0.00 0.01204003 1.794979 0.0009087173 0.2013806
cnvi0021553-126_T_R_1525544974 NC 0.00 0.01386864 1.840978 0.00 0.2507177
cnvi0007381-126_B_R_1514269228 NC 0.00 0.03813872 2.058155 0.00 0.1949465
cnvi0019138-126_B_R_1525543195 NC 0.00 0.99917 1.551797 1 0.08188924
cnvi0021554-126_T_F_1525544906 NC 0.00 0.03156658 1.800996 0.00 0.217418

Total number of rows: 1199187

Table truncated, full table size 92664 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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