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Sample GSM315240 Query DataSets for GSM315240
Status Public on Sep 24, 2008
Title GenomoPhi-amplified gDNA, 0.5ng, 04-018
Sample type genomic
 
Source name 0.5 ng of 04-018 gDNA, amplified using GenomoPhi v2
Organism Homo sapiens
Characteristics Partially degraded genomic DNA sample 04-018 has known CNVs.
Biomaterial provider Beverly S. Emanuel
Treatment protocol The gDNA was amplified with the GenomiPhi v2 kit (GE Healthcare Life Sciences) with 0.5 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 5721 122 AA 0.7355374 0.001085583 2.346488 0 -0.9603488
MitoA10551G-13273286_T_F_IFB1141639111:0 7900 524 AA 0.7127789 0.02151531 3.349395 0 -0.7414714
MitoA11252G-13273288_B_R_IFB1141661584:0 9887 497 AA 0.7452475 0.01489333 4.156027 0 -0.4736312
MitoA11468G-13273289_B_R_IFB1141719645:0 682 7663 BB 0.7344813 0.9390249 2.349592 0.9875746 -0.2587157
MitoA11813G-13273292_T_F_IFB1141667833:0 7369 994 AA 0.6571591 0.05129981 3.260713 0.008280313 -0.6730306
MitoA12309G-13273294_T_F_IFB1141664161:0 705 6476 BB 0.7016401 0.9215755 2.03358 1 -0.3918138
MitoA13106G-13273298_B_R_IFB1141641623:0 2917 186 AA 0.7644064 0.01708227 1.215291 0 -0.3673588
MitoA13264G-13273299_T_F_IFB1141660858:0 8909 683 AA 0.6638212 0.02624144 3.806355 0 -0.8226569
MitoA13781G-13273301_T_F_IFB1141687043:0 585 168 AA 0.761773 0.09984758 0.2549826 0.06037432 -2.321056
MitoA14234G-13273304_T_F_IFB1141674277:0 5304 234 AA 0.7340815 0.01084619 2.206358 0 -0.5849632
MitoA14583G-13273306_T_F_IFB1141688843:0 2800 172 AA 0.74575 0.01582825 1.163521 0.003754854 -0.9625011
MitoA15219G-13273311_T_F_IFB1141717824:0 1114 7383 BB 0.7043204 0.8821279 2.449808 0.9539522 -0.5724775
MitoA15245G-13273312_B_R_IFB1141677374:0 3558 332 AA 0.7352474 0.03103849 1.517925 0 -0.8305548
MitoA15302G-13273313_T_F_IFB1141686491:0 924 7002 BB 0.6843253 0.8997476 2.267511 1 -0.3308257
MitoA15759G-13273316_B_R_IFB1141715135:0 9722 478 AA 0.7630112 0.01438651 4.08322 0.003184616 -0.6367697
MitoA15925G-13273318_T_F_IFB1141694300:0 6073 545 AA 0.7037888 0.03118154 2.606667 0 -0.5959983
MitoA16163G-13273319_T_F_IFB1141711520:0 7925 1405 AA 0.6588464 0.06985497 3.601177 0.02756128 -0.8318513
MitoA16164G-13273320_T_F_IFB1141715312:0 6199 412 AA 0.7340815 0.02104827 2.621823 0.004749598 -0.777262
MitoA1738G-13273322_T_F_IFB1141639534:0 8924 550 AA 0.7161461 0.01968438 3.776036 0 -0.6974289
MitoA3349G-13273328_T_F_IFB1141711832:0 11586 1278 AA 0.7037888 0.0412774 5.066197 0.01181539 -0.4754845

Total number of rows: 561466

Table truncated, full table size 52394 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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