Beadstudio tool

Manufactured by Illumina

Sourced in United States

BeadStudio is a software tool that provides a graphical user interface for analyzing data from Illumina's microarray products. It allows users to import, visualize, and interpret the results of genetic studies conducted using Illumina's microarray platforms.

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Lab products found in correlation

Geneseek porcine 50k snp chip, by Neogen (2 mentions)

2 protocols using beadstudio tool

Genome-wide SNP Genotyping of Porcine Samples

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We used the phenol-chloroform method to extract genomic DNA from blood. Genotyping of a total number of 50,703 SNPs across the whole genome was performed using the GeneSeek Porcine 50 K SNP Chip (Neogen, Lincoln, NE, United States ). We performed the following quality control through PLINK (V1.90) software (Purcell et al., 2007 (link)) and determined the numbers of SNPs in the following categories: 1) SNPs with minor allele frequencies (MAF) ≥5% and 2) SNPs and individual call rates ≥95%. Only autosomal SNPs, with a total number of 40,070 SNPs, were considered for subsequent analyses. The genotyping module of BeadStudio tool (Illumina, Inc., San Diego, CA, United States) was used to determine the genotypes signal intensity of the individuals, including log R ratio (LRR) and B-allele frequency (BAF).

Wang Z., Guo Y., Liu S, & Meng Q. (2021). Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population. Frontiers in Genetics, 12, 753748.

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Whole-Genome SNP Genotyping of Porcine Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

We used the phenol-chloroform method to extract genomic DNA from blood. Genotyping of a total number of 50,703 SNPs across the whole genome was performed using the GeneSeek Porcine 50K SNP Chip (Neogen, Lincoln, NE, USA). We performed the following quality control through PLINK (V1.90) software (Purcell et al., 2007) (link) and determined the numbers of SNPs in the following categories: (1) SNPs with minor allele frequencies (MAF) 5% and (2) SNPs and individual call rates 95%. Only autosomal SNPs, with a total number of 40,070 SNPs, were considered for subsequent analyses. The genotyping module of BeadStudio tool (Illumina, Inc., San Diego, CA, USA) was used to determine the genotypes signal intensity of the individuals, including log R ratio (LRR) and B-allele frequency (BAF).

Wang Z., Guo Y., Wang T., Zhang C., Liu S., Zhang B., Li X., Liang Y., Zhu Q., Wang W., Zhang Q., Wang X., & Meng Q. (2020). Genome-wide assessment characteristics of genes overlapping copy number variation regions in Duroc purebred population.

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