NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM315254 Query DataSets for GSM315254
Status Public on Sep 24, 2008
Title GenomoPhi-amplified gDNA, 0.5ng, 05-050
Sample type genomic
 
Source name 0.5 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 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 8664 92 AA 0.7355374 0 2.058645 0 -1.149157
MitoA10551G-13273286_T_F_IFB1141639111:0 9375 430 AA 0.7127789 0.01512589 2.280241 0 -1.296185
MitoA11252G-13273288_B_R_IFB1141661584:0 12412 424 AA 0.7452475 0.009591632 2.995115 0 -0.946225
MitoA11468G-13273289_B_R_IFB1141719645:0 14131 780 AA 0.7344813 0.02046908 3.467415 0.003779439 -0.8536131
MitoA11813G-13273292_T_F_IFB1141667833:0 11143 921 AA 0.6571591 0.03413537 2.789511 0 -0.8982056
MitoA12309G-13273294_T_F_IFB1141664161:0 8315 765 AA 0.7016401 0.03840231 2.09341 0.0186681 -1.241607
MitoA13106G-13273298_B_R_IFB1141641623:0 4392 1132 NC 0.7644064 0.1201853 1.237623 0.1104138 -0.3410889
MitoA13264G-13273299_T_F_IFB1141660858:0 14108 726 AA 0.6638212 0.0185639 3.451825 0 -0.9637076
MitoA13781G-13273301_T_F_IFB1141687043:0 485 134 NC 0.761773 0.1031079 0.1286042 0.06422659 -3.308517
MitoA14234G-13273304_T_F_IFB1141674277:0 10375 268 AA 0.7340815 0.00508391 2.4855 0 -0.4130937
MitoA14583G-13273306_T_F_IFB1141688843:0 3905 149 AA 0.74575 0.008713716 0.9377275 0 -1.273757
MitoA15219G-13273311_T_F_IFB1141717824:0 9640 1007 AA 0.7043204 0.04499774 2.451356 0 -1.074266
MitoA15245G-13273312_B_R_IFB1141677374:0 6123 504 AA 0.7352474 0.03277822 1.527483 0 -0.8214988
MitoA15302G-13273313_T_F_IFB1141686491:0 1016 10531 BB 0.6843253 0.9312649 2.211353 1 -0.2013389
MitoA15759G-13273316_B_R_IFB1141715135:0 13518 410 AA 0.7630112 0.007749421 3.253229 0 -0.9646046
MitoA15925G-13273318_T_F_IFB1141694300:0 10675 599 AA 0.7037888 0.02056014 2.618549 0 -0.5894371
MitoA16163G-13273319_T_F_IFB1141711520:0 12931 1612 AA 0.6588464 0.05565869 3.341153 0.01085391 -0.939974
MitoA16164G-13273320_T_F_IFB1141715312:0 8608 358 AA 0.7340815 0.01278846 2.085857 0 -1.107192
MitoA1738G-13273322_T_F_IFB1141639534:0 1949 9944 NC 0.7161461 0.8538415 2.320796 0.9119994 -1.399682
MitoA3349G-13273328_T_F_IFB1141711832:0 16049 1122 AA 0.7037888 0.02809557 3.983994 0 -0.8221722

Total number of rows: 561466

Table truncated, full table size 51443 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap