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Sample GSM315241 Query DataSets for GSM315241
Status Public on Sep 24, 2008
Title GenomoPhi-amplified gDNA, 5ng, 04-018
Sample type genomic
 
Source name 5 ng of 04-018 gDNA, amplified using GenomoPhi v2
Organism Homo sapiens
Characteristics Partially degraded genomic DNA sample 04-018 has known CNVs.
Treatment protocol The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Sciences) with 5 ng gDNA as input, using the protocol provided with the kit. 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 12680 279 AA 0.7355374 0.006370287 2.546314 0.000661778 -0.8424411
MitoA10551G-13273286_T_F_IFB1141639111:0 15282 860 AA 0.7127789 0.02701908 3.167748 0.003740222 -0.8219144
MitoA11252G-13273288_B_R_IFB1141661584:0 15109 768 AA 0.7452475 0.02376758 3.116586 0.005942986 -0.8888696
MitoA11468G-13273289_B_R_IFB1141719645:0 962 10200 BB 0.7344813 0.9425118 2.060192 0.9918093 -0.4483474
MitoA11813G-13273292_T_F_IFB1141667833:0 15290 1834 AA 0.6571591 0.06475159 3.348978 0.02405694 -0.6344972
MitoA12309G-13273294_T_F_IFB1141664161:0 1292 9214 BB 0.7016401 0.9116048 1.943552 1 -0.4838001
MitoA13106G-13273298_B_R_IFB1141641623:0 6478 312 AA 0.7644064 0.02051734 1.326611 0 -0.2409157
MitoA13264G-13273299_T_F_IFB1141660858:0 18909 1294 AA 0.6638212 0.03447552 3.964653 0.007135962 -0.7638724
MitoA13781G-13273301_T_F_IFB1141687043:0 2292 238 AA 0.761773 0.04854485 0.4856225 0 -1.39162
MitoA14234G-13273304_T_F_IFB1141674277:0 9925 394 AA 0.7340815 0.01648892 2.023015 0 -0.7101225
MitoA14583G-13273306_T_F_IFB1141688843:0 7100 208 AA 0.74575 0.009523821 1.430363 0 -0.6646162
MitoA15219G-13273311_T_F_IFB1141717824:0 2032 12240 BB 0.7043204 0.8939348 2.647938 0.9671069 -0.4427428
MitoA15245G-13273312_B_R_IFB1141677374:0 9601 896 AA 0.7352474 0.04831026 2.05157 0.008886735 -0.3959267
MitoA15302G-13273313_T_F_IFB1141686491:0 2107 12485 BB 0.6843253 0.8920793 2.70795 1 -0.1123198
MitoA15759G-13273316_B_R_IFB1141715135:0 20319 882 AA 0.7630112 0.01967287 4.16734 0.009057076 -0.6073502
MitoA15925G-13273318_T_F_IFB1141694300:0 12695 900 AA 0.7037888 0.0354594 2.663819 0.004662194 -0.5647086
MitoA16163G-13273319_T_F_IFB1141711520:0 17180 2609 AA 0.6588464 0.08364584 3.86547 0.04379153 -0.7296759
MitoA16164G-13273320_T_F_IFB1141715312:0 11857 651 AA 0.7340815 0.02585015 2.452267 0.01013038 -0.8737163
MitoA1738G-13273322_T_F_IFB1141639534:0 15933 923 AA 0.7161461 0.02805264 3.308034 0.009047325 -0.8883272
MitoA3349G-13273328_T_F_IFB1141711832:0 19925 1809 AA 0.7037888 0.0477842 4.260448 0.0192781 -0.7253824

Total number of rows: 561466

Table truncated, full table size 51746 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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