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Sample GSM4605936 Query DataSets for GSM4605936
Status Public on Aug 23, 2021
Title Ami134
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)
Ami134.Score
Ami134.Theta
Ami134.R
Ami134.B Allele Freq
Ami134.Log R Ratio

Data table
ID_REF VALUE Ami134.Score Ami134.Theta Ami134.R Ami134.B Allele Freq Ami134.Log R Ratio
rs1000000 BB 0.7878883 0.9663093 1.636133 0.9870244 0.08264285
rs1000002 AB 0.8657144 0.5684831 1.159827 0.623279 0.1239526
rs10000023 AB 0.7550569 0.4853272 2.459517 0.5252329 0.138643
rs1000003 AB 0.7900333 0.4412226 1.767877 0.5308682 -0.01766133
rs10000030 BB 0.7818998 0.9589351 0.5956129 0.962455 -0.3932357
rs10000037 BB 0.8993763 0.9569505 1.051748 1 0.02264127
rs10000041 AA 0.9236166 0.03340731 1.224395 0.004369484 0.1427123
rs10000042 AB 0.7844193 0.64414 1.104073 0.6074375 0.06174183
rs10000049 AA 0.4321642 0.02782878 1.400253 0.00 0.1614222
rs1000007 AA 0.908865 0.009731469 1.02013 0.00 0.1194448
rs10000073 AA 0.9258915 0.01110634 1.062468 0.00 -0.01513151
rs10000081 AA 0.9052351 0.04819587 0.8327804 0.0165984 -0.03262623
rs10000092 AB 0.839045 0.4205471 0.8593072 0.4546597 -0.2288031
rs10000105 BB 0.4757184 0.9050455 0.9115196 0.9128591 -0.2176882
rs10000119 BB 0.8178427 0.9158006 1.054981 0.927789 -0.3051846
rs10000124 BB 0.8103635 0.9517835 1.693088 0.9796705 0.1455942
rs10000154 AA 0.9269766 0.02909205 1.229532 0.01131649 0.3224787
rs1000016 AB 0.8704742 0.4954482 1.170197 0.5378232 -0.3730766
rs10000160 BB 0.9014667 0.9484863 1.19941 0.9812371 0.1689749
rs10000169 AB 0.9196957 0.5887353 1.376984 0.5385716 0.190464

Total number of rows: 713014

Table truncated, full table size 43370 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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