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Sample GSM4605937 Query DataSets for GSM4605937
Status Public on Aug 23, 2021
Title Ami136
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)
Ami136.Score
Ami136.Theta
Ami136.R
Ami136.B Allele Freq
Ami136.Log R Ratio

Data table
ID_REF VALUE Ami136.Score Ami136.Theta Ami136.R Ami136.B Allele Freq Ami136.Log R Ratio
rs1000000 AB 0.7878883 0.399138 1.594002 0.4681936 -0.4672445
rs1000002 AB 0.879837 0.5330573 0.8721811 0.5907524 -0.2978492
rs10000023 AB 0.7550569 0.4989374 2.335264 0.5388277 0.07434304
rs1000003 AA 0.7900333 0.04451371 1.753237 0.01353433 0.09794081
rs10000030 AB 0.7818998 0.6914288 0.9940948 0.5199925 0.3440027
rs10000037 BB 0.8993763 0.9634806 1.06416 1 0.04580248
rs10000041 AB 0.9236166 0.3686412 1.113111 0.3855028 -0.05668562
rs10000042 AA 0.7844193 0.1017765 1.026909 0.03321219 0.07658272
rs10000049 AB 0.3143363 0.4796126 1.346563 0.6227716 -0.1392713
rs1000007 AA 0.908865 0.02568537 1.118832 0.004416838 0.2444305
rs10000073 AA 0.9258915 0.01954841 1.066563 0.00 -0.01417013
rs10000081 AA 0.9052351 0.08031091 0.8429839 0.05057988 -0.02802343
rs10000092 AB 0.8295506 0.3583702 1.158211 0.3828489 0.2195222
rs10000105 BB 0.8648784 0.9550891 0.9929354 0.9756774 -0.06349595
rs10000119 AB 0.9077633 0.61715 1.714371 0.5423665 0.2224684
rs10000124 BB 0.8103635 0.9586901 1.565166 0.9861336 0.04057284
rs10000154 AB 0.9269766 0.484654 1.405739 0.4618194 0.3165482
rs1000016 AB 0.8704742 0.4595633 1.285751 0.5033444 -0.2608841
rs10000160 BB 0.9014667 0.9632063 1.18062 0.9988884 0.1580552
rs10000169 BB 0.9196957 0.973626 1.227165 0.9932895 0.2146277

Total number of rows: 713014

Table truncated, full table size 43267 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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