Comment[GEAAccession]	E-GEAD-406
MAGE-TAB Version	1.1
Investigation Title	Affymetrix SNP array data for wheat samples
Experiment Description	The genotypes of 191 common wheat accessions were characterized by a high density Wheat660K array. Based on the quality preprocessing results provided by PLINK software ,8,451 and 221,878 SNPs were removed for having call rates less than 80% and minor allele frequencies less than 0.05, respectively. No accession was removed for low genotyping (MIND > 0.1). Finally, 191 common wheat accessions containing 387,537 SNPs were retained and could be used for further analyses.
Experimental Design	genotype design	population based design	genotyping design	array specific design
Experimental Factor Name	isolate
Experimental Factor Type	isolate
Person Last Name	Pan
Person First Name	Hu
Person Affiliation	Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Person Roles	submitter
Public Release Date	2024-09-18
PubMed ID	33413113
Protocol Name	P-GEAD-696	P-GEAD-697	P-GEAD-698	P-GEAD-699	P-GEAD-700	P-GEAD-701
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	The plant material was a collection of 191 wheat accessions including five introduced varieties, ten landraces and 176 improved cultivars. And all the plant materials were provided by the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences.	Genomic DNA was extracted from leaf of 191 wheat assessions using a CTAB method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer,and agarose gel electrophoresis.	As per manufacturer (Affymetrix)	DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.	The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix software APT 1.17.0.	The array image was acquired using Affymetrix SNPolisher 1.5.0 Software.This quality preprocessing of genotyping data was completed using PLINK software. Genotype Call (SNP call): A=AA, C=CC, T=TT, G=GG, R=AG, Y=CT, S=CG, W=AT, K=GT, M=AC, N=Unknown.
SDRF File	E-GEAD-406.sdrf.txt
Comment[Number of channel]	dual-channel
Comment[Array Design REF]	A-GEAD-13
Comment[AEExperimentType]	genotyping by array
Comment[BioProject]	PRJDB10577
Comment[Last Update Date]	2024-09-18