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Sample GSM315242 Query DataSets for GSM315242
Status Public on Sep 24, 2008
Title Native gDNA, 04-018
Sample type genomic
 
Source name Native 04-018 gDNA
Organism Homo sapiens
Characteristics Partially degraded genomic DNA sample 04-018 has known CNVs.
Treatment protocol No treatment.
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 17932 504 AA 0.7355374 0.01043737 3.918726 0.005137678 -0.2204671
MitoA10551G-13273286_T_F_IFB1141639111:0 18117 1427 AA 0.7127789 0.03982458 4.137559 0.01825468 -0.436592
MitoA11252G-13273288_B_R_IFB1141661584:0 16656 1073 AA 0.7452475 0.03141207 3.756509 0.0145327 -0.6194437
MitoA11468G-13273289_B_R_IFB1141719645:0 1654 14398 BB 0.7344813 0.9266797 3.13819 0.9725819 0.1588066
MitoA11813G-13273292_T_F_IFB1141667833:0 14258 2162 AA 0.6571591 0.08149239 3.455475 0.04369102 -0.589334
MitoA12309G-13273294_T_F_IFB1141664161:0 2218 10829 BB 0.7016401 0.8654118 2.565478 1 -0.2007326
MitoA13106G-13273298_B_R_IFB1141641623:0 5431 423 AA 0.7644064 0.03655948 1.230922 0.0159056 -0.3489213
MitoA13264G-13273299_T_F_IFB1141660858:0 21092 2081 AA 0.6638212 0.05149279 4.900498 0.02657008 -0.4581386
MitoA13781G-13273301_T_F_IFB1141687043:0 4214 467 AA 0.761773 0.05453818 0.9793374 0.00683775 -0.3796489
MitoA14234G-13273304_T_F_IFB1141674277:0 9291 496 AA 0.7340815 0.02398089 2.070172 0.006909853 -0.6768795
MitoA14583G-13273306_T_F_IFB1141688843:0 7927 365 AA 0.74575 0.01931401 1.753172 0.007632998 -0.3710301
MitoA15219G-13273311_T_F_IFB1141717824:0 2868 12079 BB 0.7043204 0.8435491 2.947223 0.9109696 -0.361639
MitoA15245G-13273312_B_R_IFB1141677374:0 7442 978 AA 0.7352474 0.06857455 1.768577 0.03246927 -0.6100658
MitoA15302G-13273313_T_F_IFB1141686491:0 2738 11987 BB 0.6843253 0.8495439 2.901565 1 -0.2050653
MitoA15759G-13273316_B_R_IFB1141715135:0 20581 1151 AA 0.7630112 0.02673397 4.610623 0.01690105 -0.4615153
MitoA15925G-13273318_T_F_IFB1141694300:0 12924 1238 AA 0.7037888 0.04920327 2.990851 0.02044189 -0.3976489
MitoA16163G-13273319_T_F_IFB1141711520:0 19718 2893 AA 0.6588464 0.07906979 4.764536 0.03840605 -0.4279842
MitoA16164G-13273320_T_F_IFB1141715312:0 14547 922 AA 0.7340815 0.0306216 3.276382 0.01547707 -0.4557284
MitoA1738G-13273322_T_F_IFB1141639534:0 16606 1275 AA 0.7161461 0.0385676 3.78506 0.02089262 -0.6939853
MitoA3349G-13273328_T_F_IFB1141711832:0 21079 2252 AA 0.7037888 0.05620884 4.930935 0.02894041 -0.5145264

Total number of rows: 561466

Table truncated, full table size 51788 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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