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Sample GSM315252 Query DataSets for GSM315252
Status Public on Sep 24, 2008
Title Wpa-amplified gDNA, 5ng, 05-050
Sample type genomic
 
Source name 5 ng of 05-050 gDNA, amplified using Wpa
Organism Homo sapiens
Characteristics Good-quality genomic DNA sample 05-050 has known CNVs.
Treatment protocol The gDNA was amplified with Wpa (a new WGA procedure as described in the citation) with 5 ng gDNA as input. The amplicon was purified with the QIAEXII kit from Qiagen.
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using an extraction kit.
Label C-Bio and A-DNP
Label protocol SNPs were identified by single-base extension. SNPs were analyzed at the Yale Keck Laboratory (http://keck.med.yale.edu/)
 
Hybridization protocol Hybridization was performed at the Yale Keck Laboratory.
Scan protocol Scan was performed at the Yale Keck Laboratory.
Description SNP genotyping was performed at the Yale Keck Laboratory.
Data processing Data processing was performed using BeadStudio software (Illumina) v3.
 
Submission date Aug 22, 2008
Last update date Sep 23, 2008
Contact name Xinghua Pan
E-mail(s) xinghua.pan@yale.edu
Phone 203-7372616
Organization name Yale University School of Medicine
Department Department of Genetics
Lab Sherman Weissman
Street address 300 Cedar Street, TAC-S320
City New Haven
State/province CT
ZIP/Postal code CT
Country USA
 
Platform ID GPL6982
Series (2)
GSE12732 Evaluation of the amplicons for SNP typing (allele bias) and locus bias using Illumina 550-Duo BeadChip
GSE12751 Evaluation of Wpa-generated amplicons for SNP typing (allele bias), locus bias, and detection of known CNVs

Data table header descriptions
ID_REF
X raw Raw, un-normalized A allele signal
Y raw Raw, un-normalized B allele signal
VALUE Genotype: AA, AB, BB, or NC (no call)
Confidence_Score BeadStudio confidence score
Theta BeadStudio genotype metric
R BeadStudio intensity metric
B_Allele_Freq BeadStudio estimate of B allele frequency
Log_R_ratio BeadStudio metric for signal intensity

Data table
ID_REF X raw Y raw VALUE Confidence_Score Theta R B_Allele_Freq Log_R_ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 11375 261 AA 0.7355374 0.004574496 3.576622 0 -0.3522541
MitoA10551G-13273286_T_F_IFB1141639111:0 13009 888 AA 0.7127789 0.03084637 4.254642 0.008078285 -0.3963343
MitoA11252G-13273288_B_R_IFB1141661584:0 13288 1005 AA 0.7452475 0.03511656 4.373178 0.01869523 -0.4001541
MitoA11468G-13273289_B_R_IFB1141719645:0 15384 787 AA 0.7344813 0.02094509 4.958322 0.004236246 -0.3368892
MitoA11813G-13273292_T_F_IFB1141667833:0 11535 1427 AA 0.6571591 0.06288536 3.950511 0.02186817 -0.3961786
MitoA12309G-13273294_T_F_IFB1141664161:0 11126 678 AA 0.7016401 0.02659484 3.615983 0.005325679 -0.4530747
MitoA13106G-13273298_B_R_IFB1141641623:0 5010 534 AA 0.7644064 0.05293038 1.691405 0.03440689 0.1095608
MitoA13264G-13273299_T_F_IFB1141660858:0 13078 1295 AA 0.6638212 0.04864548 4.389202 0.02331839 -0.6171084
MitoA13781G-13273301_T_F_IFB1141687043:0 2673 295 AA 0.761773 0.05499062 0.9047844 0.007372343 -0.4938807
MitoA14234G-13273304_T_F_IFB1141674277:0 7191 365 AA 0.7340815 0.0206579 2.316379 0.003180011 -0.5147585
MitoA14583G-13273306_T_F_IFB1141688843:0 5984 533 AA 0.74575 0.04282821 1.99124 0.03379417 -0.1873308
MitoA15219G-13273311_T_F_IFB1141717824:0 10599 2069 AA 0.7043204 0.1038083 3.840825 0.05585645 -0.4264297
MitoA15245G-13273312_B_R_IFB1141677374:0 7203 1170 AA 0.7352474 0.08509164 2.544171 0.05169101 -0.08545922
MitoA15302G-13273313_T_F_IFB1141686491:0 2018 11696 BB 0.6843253 0.8931233 3.876754 1 0.4103883
MitoA15759G-13273316_B_R_IFB1141715135:0 15060 1152 AA 0.7630112 0.03562198 4.960097 0.02677448 -0.3561087
MitoA15925G-13273318_T_F_IFB1141694300:0 11447 883 AA 0.7037888 0.03597966 3.771959 0.005259513 -0.06289098
MitoA16163G-13273319_T_F_IFB1141711520:0 13460 2595 AA 0.6588464 0.1024488 4.868798 0.06592048 -0.3967544
MitoA16164G-13273320_T_F_IFB1141715312:0 11150 714 AA 0.7340815 0.02838967 3.633399 0.01297606 -0.3065122
MitoA1738G-13273322_T_F_IFB1141639534:0 1028 10083 BB 0.7161461 0.9418715 3.122687 1 -0.9715136
MitoA3349G-13273328_T_F_IFB1141711832:0 14498 1918 AA 0.7037888 0.06783938 5.000169 0.0422796 -0.4944108

Total number of rows: 561466

Table truncated, full table size 52350 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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