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Sample GSM315255 Query DataSets for GSM315255
Status Public on Sep 24, 2008
Title GenomoPhi-amplified gDNA, 5ng, 05-050
Sample type genomic
 
Source name 5 ng of 05-050 gDNA, amplified using GenomoPhi v2
Organism Homo sapiens
Characteristics Good-quality genomic DNA sample 05-050 has known CNVs.
Treatment protocol The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Science) 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 5469 146 NC 0.7355374 0.005207289 1.666941 0 -1.453648
MitoA10551G-13273286_T_F_IFB1141639111:0 13109 519 AA 0.7127789 0.01214996 4.04695 0 -0.4685367
MitoA11252G-13273288_B_R_IFB1141661584:0 12911 518 AA 0.7452475 0.01237773 3.98709 0 -0.5335001
MitoA11468G-13273289_B_R_IFB1141719645:0 12801 418 AA 0.7344813 0.008991244 3.932944 0 -0.6894134
MitoA11813G-13273292_T_F_IFB1141667833:0 12810 1326 AA 0.6571591 0.04105132 4.126404 0 -0.333333
MitoA12309G-13273294_T_F_IFB1141664161:0 7594 352 AA 0.7016401 0.01464588 2.350401 0 -1.074556
MitoA13106G-13273298_B_R_IFB1141641623:0 5100 822 AA 0.7644064 0.06598724 1.697786 0.04916285 0.1149939
MitoA13264G-13273299_T_F_IFB1141660858:0 14752 972 AA 0.6638212 0.02413729 4.63709 0 -0.5378473
MitoA13781G-13273301_T_F_IFB1141687043:0 770 151 AA 0.761773 0.07188778 0.252356 0.02733764 -2.335995
MitoA14234G-13273304_T_F_IFB1141674277:0 6550 309 AA 0.7340815 0.01480493 2.026849 0 -0.7073913
MitoA14583G-13273306_T_F_IFB1141688843:0 3764 172 AA 0.74575 0.01297722 1.15875 0.000582883 -0.968429
MitoA15219G-13273311_T_F_IFB1141717824:0 10046 1206 AA 0.7043204 0.04831696 3.268503 0 -0.6592159
MitoA15245G-13273312_B_R_IFB1141677374:0 4140 413 AA 0.7352474 0.03777189 1.322653 0 -1.029221
MitoA15302G-13273313_T_F_IFB1141686491:0 1204 10977 BB 0.6843253 0.9190136 2.657382 1 -0.002939039
MitoA15759G-13273316_B_R_IFB1141715135:0 13037 511 AA 0.7630112 0.01196687 4.023579 0.00049671 -0.6579979
MitoA15925G-13273318_T_F_IFB1141694300:0 8626 573 AA 0.7037888 0.02389987 2.707731 0 -0.5411201
MitoA16163G-13273319_T_F_IFB1141711520:0 7516 1284 AA 0.6588464 0.07090387 2.522693 0.02879572 -1.345355
MitoA16164G-13273320_T_F_IFB1141715312:0 8179 325 AA 0.7340815 0.01174429 2.520968 0 -0.8338543
MitoA1738G-13273322_T_F_IFB1141639534:0 1167 10065 BB 0.7161461 0.913601 2.454646 0.9751339 -1.318786
MitoA3349G-13273328_T_F_IFB1141711832:0 12541 1202 AA 0.7037888 0.03756946 4.019314 0.007562713 -0.8094383

Total number of rows: 561466

Table truncated, full table size 52336 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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