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Sample GSM4605949 Query DataSets for GSM4605949
Status Public on Aug 23, 2021
Title AmiA47B
Sample type genomic
 
Source name blood
Organism Homo sapiens
Characteristics population: Ami
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)
AmiA47B.Score
AmiA47B.Theta
AmiA47B.R
AmiA47B.B Allele Freq
AmiA47B.Log R Ratio

Data table
ID_REF VALUE AmiA47B.Score AmiA47B.Theta AmiA47B.R AmiA47B.B Allele Freq AmiA47B.Log R Ratio
rs1000000 BB 0.7878883 0.9838678 1.635046 1 0.1025146
rs1000002 AA 0.879837 0.02063377 0.7838269 0.005138436 -0.3955345
rs10000023 AA 0.7550569 0.01399901 2.06626 0.00 0.1642697
rs1000003 AB 0.7900333 0.3785575 1.882467 0.4624273 0.05832474
rs10000030 BB 0.7818998 0.9785213 0.9442759 0.994851 0.2717273
rs10000037 BB 0.8993763 0.9728773 1.156676 1 0.1750934
rs10000041 AA 0.9236166 0.03740249 1.146039 0.008911679 0.04654536
rs10000042 BB 0.7844193 0.9646048 1.023115 0.9961532 0.08852252
rs10000049 AA 0.4321642 0.04500484 1.192463 0.00784542 -0.0836621
rs1000007 AA 0.908865 0.008560362 1.169265 0.00 0.3169016
rs10000073 AA 0.9258915 0.0279975 1.001737 0.00 -0.1092128
rs10000081 AB 0.9052351 0.5484815 0.8988977 0.5466905 -0.07341779
rs10000092 AB 0.839045 0.4267879 0.9611181 0.4618675 -0.06902532
rs10000105 BB 0.8648784 0.9363531 1.094913 0.9521587 0.06595316
rs10000119 BB 0.9077633 0.9718523 1.269492 1 -0.003277065
rs10000124 BB 0.8103635 0.9622153 1.360609 0.9894323 -0.1572249
rs10000154 AB 0.9269766 0.523755 1.227987 0.5005468 0.10609
rs1000016 BB 0.8704742 0.9892627 1.175078 1 0.005542316
rs10000160 BB 0.9014667 0.9556481 0.9880419 0.9898251 -0.1049473
rs10000169 BB 0.9196957 0.9795186 1.083135 1 0.03763107

Total number of rows: 713014

Table truncated, full table size 42654 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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