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Sample GSM4605945 Query DataSets for GSM4605945
Status Public on Aug 23, 2021
Title AmiA22
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)
AmiA22.Score
AmiA22.Theta
AmiA22.R
AmiA22.B Allele Freq
AmiA22.Log R Ratio

Data table
ID_REF VALUE AmiA22.Score AmiA22.Theta AmiA22.R AmiA22.B Allele Freq AmiA22.Log R Ratio
rs1000000 BB 0.7878883 0.9861103 1.631292 1 0.1018805
rs1000002 AB 0.5630228 0.6263962 0.9922836 0.6764525 -0.08365007
rs10000023 AA 0.7550569 0.01580048 1.921116 0.00 0.05786467
rs1000003 AA 0.7900333 0.02329881 1.544558 0.00 -0.0753628
rs10000030 BB 0.7818998 0.9866257 0.8052188 1 0.04195336
rs10000037 AB 0.8993763 0.4046853 1.457594 0.4794368 0.06283174
rs10000041 AA 0.9236166 0.04060792 0.9907532 0.01255599 -0.1641173
rs10000042 AB 0.7844064 0.6760428 0.983198 0.6461348 -0.09250159
rs10000049 AA 0.4321642 0.0327993 1.317992 0.00 0.07020269
rs1000007 AA 0.908865 0.009513559 1.12209 0.00 0.256993
rs10000073 AB 0.9258915 0.5541856 1.166792 0.5021484 -0.1471457
rs10000081 AB 0.9052351 0.5530995 0.8970256 0.5516547 -0.07392593
rs10000092 BB 0.839045 0.9393009 0.8175091 1 -0.08122982
rs10000105 BB 0.8648784 0.9536574 1.00539 0.9738803 -0.04640111
rs10000119 AB 0.9077633 0.5704895 1.462908 0.487291 -0.0180357
rs10000124 BB 0.8103635 0.9619276 1.471991 0.9891632 -0.04405661
rs10000154 AB 0.9269766 0.5040594 1.198315 0.4810092 0.07832447
rs1000016 AA 0.8704742 0.009795734 1.29017 0.00 -0.1101423
rs10000160 BB 0.9014667 0.9651506 0.9453068 1 -0.1610612
rs10000169 BB 0.9196957 0.9871986 1.214932 1 0.2073677

Total number of rows: 713014

Table truncated, full table size 42080 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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