Axiom Sugarcane100K SNP array data for sugarcane mapping population
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PROVIDER: PRJNA527787 | ENA |
REPOSITORIES: ENA
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Project description:To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including one F1 population derived from cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.
2019-12-17 | GSE128450 | GEO
Project description:MDS patients are characterized as the deletion in chromosome 17. We generated induced pluripotent stem cells (iPSCs) from MDS fibroblasts. We performed SNP microarray analysis using Affymetrix axiom EUR array platform.
2013-11-26 | GSE52691 | GEO
Project description:MDS patients are characterized as the deletion in chromosome 17. We generated induced pluripotent stem cells (iPSCs) from MDS fibroblasts. We performed SNP microarray analysis using Affymetrix axiom EUR array platform. Affymetrix axiom EUR arrays were performed according to the manufacturer's directions on DNA extracted from MDS fibroblasts and iPSCs.
2013-11-26 | E-GEOD-52691 | biostudies-arrayexpress
Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).
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Project description:The Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community.
2017-03-22 | GSE94633 | GEO
Project description:Axiom Genome-Wide Chicken Array of Broiler Chickens
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Project description: Not available
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Project description:allele call files from analysis of NCI60 cell line DNA on 100K SNP arrays. Keywords = NCI60, SNP array, cancer cell line Keywords: other
2005-07-02 | GSE2520 | GEO
Project description:Transdisciplinary Research Into Cancer of the Lung (TRICL): Affymetrix Axiom Array
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Project description:The current study examined the association between genotype and resistance training-induced changes in dual energy x-ray absorptiometry (DXA) derived lean soft-tissue mass (LSTM) and skeletal muscle fiber cross-sectional area (fCSA). Over 315,000 genetic polymorphisms were interrogated using DNA microarrays. Genome-wide association studies (GWAS) were performed to identify novel targets to reveal associations with PRE- to POST-training change scores in mean LSTM and fCSA. The first GWAS indicated no single nucleotide polymorphisms (SNP) associated with DXA derived LSTM. The second GWAS indicated two SNPs associated with changes in mean fCSA. While the first target identified (chr2:205936849 [GRCh38.p12]) was not annotated the second target identified (chr7:41971865 [GRCh38.p12]) was identified as an intron variant of the GLI Family Zinc Finger 3 (GLI3) gene. Follow-up analyses indicated fCSA increases were greater in the T/C and C/C GLI3 genotypes than the T/T GLI3 genotype.
2022-01-03 | GSE169300 | GEO