Bioruptor ngs sonicator

Manufactured by Diagenode

Sourced in United States

The Bioruptor NGS is a sonicator device used for fragmenting DNA and RNA samples. It utilizes ultrasonic waves to mechanically shear nucleic acid molecules into smaller fragments. The core function of the Bioruptor NGS is to provide a controlled and reproducible method for sample preparation prior to next-generation sequencing and other applications requiring fragmented nucleic acids.

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Lab products found in correlation

Phusion hot start 2 dna polymerase, by Thermo Fisher Scientific (2 mentions) V3 600 cycle kit, by Illumina (1 mentions) Miseq sequencer, by Illumina (1 mentions) Ampure xp bead, by Beckman Coulter (1 mentions) Dynabeads m 280 streptavidin magnetic beads, by Thermo Fisher Scientific (1 mentions) Nebnext ultra dna library prep kit, by Illumina (1 mentions) Hiseq 4000, by Illumina (1 mentions)

3 protocols using bioruptor ngs sonicator

Sequencing and Annotation of S. halichoeri Genomes

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Genomes of the 20 S. halichoeri isolates were sequenced at the Institute of Biotechnology (University of Helsinki, Finland) using next-generation sequencing platforms. Genomic DNA (0.5 mg) was sheared using a Bioruptor NGS Sonicator (Diagenode) to approximately 600 bp fragments. The fragments were polished, A-tailed, and ligated to a TruSeq truncated adapter. Purification of the ligation reaction was done using AMPure XP beads (Agencourt, Beckman Coulter). PCR of the libraries were done using Phusion Hot Start II DNA Polymerase (Thermo Fisher) and index P7 primers and full-length P5 adapter primers. The reactions were pooled and purified with AMPure XP beads. Size selection of the pool was done according to Lundin et al. [11 (link)]. The obtained library pool was paired-end sequenced on a MISeq Sequencer using the v3 600 cycle kit (Illumina).
Genomes of the 20 newly sequenced S. halichoeri strains were deposited in GenBank under the accession numbers listed in Table 1. The annotation was performed using the assembled DNA sequences of the 20 new draft genomes from these isolates. The genomes were run through an automatic annotation pipeline RAST (Rapid Annotation using Subsystem Technology) [12 (link)], followed by manual curation in few cases.

Aaltonen K., Kant R., Eklund M., Raunio-Saarnisto M., Paulin L., Vapalahti O., Grönthal T., Rantala M, & Sironen T. (2020). Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen. International Journal of Genomics, 2020, 8708305.

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Constructing RAD-seq Libraries for Population Genomics

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RAD-seq libraries were constructed for 128 individuals from 11 features (Table 1) using the bestRAD protocol (27 (link)). Samples were normalized to 250 ng in 10 μl of 1× TE. The genomic DNA was digested with Sbf I–HF restriction enzyme (NEB). Following ligation of the biotinylated bestRAD adapters, samples were multiplexed into two libraries consisting of 96 and 32 samples. Pooled DNA was sheared in a Bioruptor NGS sonicator (Diagenode) with three cycles of 30 s on/90 s off and then visualized on a fragment analyzer to ensure DNA fragments ranged from 100 to 500 bp.
The bestRAD adapters contain biotinylated ends, which bind to Dynabeads M-280 streptavidin magnetic beads (Life Technologies) to physically isolate the RADtagged DNA fragments. The RADtags were freed from the Dynabeads with Sbf I–HF digestion and resuspended in 55.5 μl of low TE. The NEBNext Ultra DNA Library Prep Kit for Illumina was used to repair blunt ends and ligate adapters. The RADtags were size-selected for 500 bp. A test library enrichment PCR was run with 5 μl of library for 15 cycles to determine the optimal number of PCR cycles. The final library enrichment PCR was run for 13 cycles with 15 μl of library. Paired-end sequencing of 150 bp was carried out across two lanes on an Illumina HiSeq 4000 at the UC Davis Genome Center.

Weston J.N., Jensen E.L., Hasoon M.S., Kitson J.J., Stewart H.A, & Jamieson A.J. (2022). Barriers to gene flow in the deepest ocean ecosystems: Evidence from global population genomics of a cosmopolitan amphipod. Science Advances, 8(43), eabo6672.

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Illumina Sequencing of A. phocae Genomes

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The Illumina platform was used to sequence the 12 A. phocae strains. The Bioruptor NGS sonicator (Diagenode, Denville, NJ, USA) was used to shear 0.5 µg of the genomic DNA to 600 bp parts, and these were then analyzed for quality. A-tails were generated and TruSeq adapter was ligated. MPure XP beads (Agencourt, Beckman Coulter) were used to purify the ligation. The library preparation PCRs were performed with Phusion Hot Start II DNA Polymerase (Thermo Fisher). The Index P7 primers were chosen with Barcosel and full-length P5 primers were added. AMPure XP beads were used to purify the reactions. They were pooled and selected for size, as described before by [13 (link)]. The Miseq Sequencer and v3600 cycle kit (Illumina, San Diego, CA, USA) were used to sequence the library.

Aaltonen K.J., Kant R., Kvist Nikolaisen N., Lindegaard M., Raunio-Saarnisto M., Paulin L., Vapalahti O, & Sironen T. (2021). Comparative Genomics of 42 Arcanobacterium phocae Strains. Antibiotics, 10(6), 740.

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