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Sample GSM4605953 Query DataSets for GSM4605953
Status Public on Aug 23, 2021
Title Yami21
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)
Yami21.Score
Yami21.Theta
Yami21.R
Yami21.B Allele Freq
Yami21.Log R Ratio

Data table
ID_REF VALUE Yami21.Score Yami21.Theta Yami21.R Yami21.B Allele Freq Yami21.Log R Ratio
rs1000000 AA 0.7878883 0.004786159 2.014625 0.00 0.1347215
rs1000002 AB 0.779027 0.5964725 1.196064 0.6489778 0.1767595
rs10000023 AB 0.7550569 0.4587725 2.072008 0.4985213 -0.1271955
rs1000003 AA 0.7900333 0.02955776 1.619562 0.00 -0.009769457
rs10000030 BB 0.7818998 0.9931274 0.7938902 1 0.02155511
rs10000037 BB 0.8993763 0.9629667 1.126362 1 0.127267
rs10000041 AA 0.9236166 0.03498897 0.999302 0.006167703 -0.1506622
rs10000042 AB 0.7844193 0.6302121 0.9973654 0.5905433 -0.0905544
rs10000049 BB 0.4321642 0.7674328 1.243643 1 -0.1673789
rs1000007 AB 0.908865 0.5414382 1.124874 0.518997 0.02366689
rs10000073 AA 0.9258915 0.02054192 0.9601605 0.00 -0.1663308
rs10000081 AB 0.9052351 0.5328783 0.9439426 0.5299178 -0.01128905
rs10000092 AB 0.839045 0.4678252 1.034401 0.5084711 0.03126723
rs10000105 BB 0.8647771 0.9337662 1.098091 0.9489114 0.06854
rs10000119 AB 0.9077633 0.626614 1.33321 0.5545803 -0.1351371
rs10000124 BB 0.8103635 0.9481273 1.436167 0.9762491 -0.09622432
rs10000154 BB 0.9269766 0.9669913 0.976678 0.9935681 0.02647279
rs1000016 BB 0.8704742 0.9823883 1.206405 1 0.03759337
rs10000160 BB 0.9014667 0.9631639 0.9950437 0.9988375 -0.08869214
rs10000169 AA 0.9196957 0.02965764 1.070633 0.00 0.09816271

Total number of rows: 713014

Table truncated, full table size 42657 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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