NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4605943 Query DataSets for GSM4605943
Status Public on Aug 23, 2021
Title AmiA20
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)
AmiA20.Score
AmiA20.Theta
AmiA20.R
AmiA20.B Allele Freq
AmiA20.Log R Ratio

Data table
ID_REF VALUE AmiA20.Score AmiA20.Theta AmiA20.R AmiA20.B Allele Freq AmiA20.Log R Ratio
rs1000000 AB 0.7878883 0.3810685 2.265549 0.4459744 0.05106403
rs1000002 AA 0.879837 0.00246883 1.074522 0.00 0.06342997
rs10000023 BB 0.7550569 0.955646 1.69123 0.9950187 0.0140329
rs1000003 AA 0.7900333 0.04554883 1.715701 0.01492534 0.06625478
rs10000030 BB 0.7818998 0.9901969 0.9461157 1 0.2746128
rs10000037 BB 0.8993763 0.9713535 1.170969 1 0.1913445
rs10000041 AA 0.9236166 0.03447953 1.206931 0.005588515 0.1217842
rs10000042 AB 0.7844193 0.5192027 1.248481 0.4625947 0.2153101
rs10000049 AA 0.4321642 0.03219581 1.205422 0.00 -0.05813093
rs1000007 AB 0.194916 0.7039047 1.145692 0.704603 0.1352095
rs10000073 AA 0.9258915 0.02183446 0.9175441 0.00 -0.2325299
rs10000081 AA 0.9052351 0.03096698 0.8747724 0.00 0.04534974
rs10000092 AB 0.839045 0.4590143 0.9576774 0.4990871 -0.08326393
rs10000105 BB 0.8648784 0.9554427 1.231522 0.9761213 0.2473949
rs10000119 AB 0.9077633 0.5380783 1.714724 0.4575116 0.2255661
rs10000124 BB 0.8084601 0.9312926 1.191659 0.9604957 -0.3854975
rs10000154 AA 0.9269766 0.01085286 1.082957 0.00 0.1479216
rs1000016 AB 0.8704742 0.5360194 1.441333 0.5768047 -0.0451893
rs10000160 BB 0.9014667 0.9610016 1.179752 0.9962447 0.1552107
rs10000169 AB 0.9196957 0.6174092 1.302715 0.5724475 0.1238202

Total number of rows: 713014

Table truncated, full table size 43152 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap