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Sample GSM4605966 Query DataSets for GSM4605966
Status Public on Aug 23, 2021
Title Yami73
Sample type genomic
 
Source name blood
Organism Homo sapiens
Characteristics population: Yami
region: East Asia
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA from blood was performed using standard extraction protocols.
Label Cy3, Cy5
Label protocol 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).
Data processing Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).
 
Submission date Jun 10, 2020
Last update date Aug 23, 2021
Contact name Tuuli Reisberg
Organization name University of Tartu
Street address Riia 23
City Tartu
ZIP/Postal code 51010
Country Estonia
 
Platform ID GPL22678
Series (2)
GSE152194 The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations
GSE152200 Aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
Yami73.Score
Yami73.Theta
Yami73.R
Yami73.B Allele Freq
Yami73.Log R Ratio

Data table
ID_REF VALUE Yami73.Score Yami73.Theta Yami73.R Yami73.B Allele Freq Yami73.Log R Ratio
rs1000000 AB 0.7878883 0.3852249 2.405944 0.4510854 0.1352454
rs1000002 AB 0.879837 0.5082629 1.31147 0.5679872 0.2832697
rs10000023 BB 0.7550569 0.9351549 1.576376 0.9745508 -0.1082674
rs1000003 AB 0.7900333 0.3804867 1.725319 0.4650198 -0.06821838
rs10000030 BB 0.7818998 0.9667944 0.721754 0.9754544 -0.1160517
rs10000037 BB 0.8993763 0.9504027 1.153085 0.9988148 0.1491249
rs10000041 AB 0.9236166 0.4537713 1.223444 0.4822888 0.0643535
rs10000042 AA 0.7788547 0.1132032 0.9017178 0.04496612 -0.1150908
rs10000049 AA 0.4321642 0.05390658 1.146143 0.02008528 -0.1476856
rs1000007 AA 0.908865 0.01014465 1.097723 0.00 0.224991
rs10000073 AA 0.9258915 0.0125381 1.035324 0.00 -0.05324683
rs10000081 BB 0.9052351 0.9523284 0.8405245 0.9808085 0.06652775
rs10000092 AA 0.839045 0.02075499 0.7987967 0.00 -0.2165392
rs10000105 BB 0.8644838 0.9332342 1.150681 0.9482435 0.135703
rs10000119 AA 0.9077633 0.02199725 1.032252 0.00 -0.2543219
rs10000124 BB 0.7613424 0.9225409 1.386992 0.9523061 -0.1768098
rs10000154 BB 0.9269766 0.9587139 1.037618 0.9843609 0.1086888
rs1000016 BB 0.8704742 0.9729568 1.176537 0.9966214 -0.006638647
rs10000160 BB 0.9014667 0.9358873 1.044188 0.9661293 -0.0410414
rs10000169 BB 0.9196957 0.9510083 1.028229 0.9665685 -0.05244769

Total number of rows: 713014

Table truncated, full table size 42892 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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