maldi-tof mass spectrometry iplex platform on the massarray-4 system  (agena bioscience)

Journal: Scientific Reports

Article Title: High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool

doi: 10.1038/s41598-018-26932-1

Figure Lengend Snippet: Location of the colonies sampled across the A . m . mellifera and C-lineage ranges. Samples of A . m . mellifera were collected in protected (Prot) and unprotected apiaries (Unp). The commercial breed Buckfast is also represented. Colonies were genotyped for the four SNP assays in the MassARRAY® MALDI-TOF platform from single individuals (SI) or pools of individuals (PI).

Article Snippet: The flanking regions (60 bp of either side) of these SNPs were used to design multiplexed assays with the software Assay Design 4.0 (Agena BioScience TM ) for genotyping using the Agena BioScience iPLEX chemistry and the MassARRAY® MALDI-TOF platform (hereafter abbreviated to iPLEX MassARRAY).

Techniques:

Journal: Scientific Reports

Article Title: High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool

doi: 10.1038/s41598-018-26932-1

Figure Lengend Snippet: Datasets of quality-proved samples used in the SNP assays’ testing and application. Samples were represented by a single individual (SI) or a pool of individuals (PI). The individuals were haploid drones (hap) or diploid workers (dip). Genotypes were generated from the four assays in the MassARRAY® MALDI-TOF platform (MA), from the GoldenGate® Assay in the Illumina’s BeadArray platform (GG), and from whole genome (WG) sequences in the Illumina’s HiSeq. 2500 platform.Vertical arrows connect the different individuals used in each test.

Article Snippet: The flanking regions (60 bp of either side) of these SNPs were used to design multiplexed assays with the software Assay Design 4.0 (Agena BioScience TM ) for genotyping using the Agena BioScience iPLEX chemistry and the MassARRAY® MALDI-TOF platform (hereafter abbreviated to iPLEX MassARRAY).

Techniques: Generated, Goldengate Assay

Journal: Scientific Reports

Article Title: High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool

doi: 10.1038/s41598-018-26932-1

Figure Lengend Snippet: Structure reconstructed by ADMIXTURE and Graphia Professional software packages for honeybees of diverse ancestry collected across Europe. Most depicted samples (415) were genotyped in the MassARRAY platform using the four assays (117 SNPs). Nine samples of A . m . carnica and seven A . m . ligustica , previously genotyped for the 117 SNP loci using the GoldenGate Assay in the BeadArray platform, were added to the structure analysis for a better representation of C-lineage diversity. Each sample corresponds to a single colony. Samples collected in the A . m . mellifera range are from protected (prot) and unprotected (unp) apiaries. ( a ) ADMIXTURE plot showing the genome partitioning into two clusters (K = 2) for each individual, represented by a vertical bar. Blue represents the A . m . mellifera cluster and orange the C-lineage cluster. The black lines separate individuals from different countries and studied groups. ( b ) Correlation network where nodes (honeybee samples) are connected with edges when r > 0.27. A total of 418 samples out of 431 formed connections in the graph. Samples coloured according to country of origin with expected lineage indicated within parentheses. Inset shows correlation network clustered using the Markov Cluster (MCL) algorithm at an inflation value of 1.2.

Article Snippet: The flanking regions (60 bp of either side) of these SNPs were used to design multiplexed assays with the software Assay Design 4.0 (Agena BioScience TM ) for genotyping using the Agena BioScience iPLEX chemistry and the MassARRAY® MALDI-TOF platform (hereafter abbreviated to iPLEX MassARRAY).

Techniques: Software, Goldengate Assay