Native barcoding kit exp nbd103

Manufactured by Oxford Nanopore

Sourced in United Kingdom

The Native Barcoding Kit EXP-NBD103 is a laboratory tool designed for DNA/RNA sample preparation. It enables the addition of unique molecular identifiers to individual DNA/RNA molecules, facilitating sample multiplexing and streamlining downstream data analysis.

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Lab products found in correlation

Minion, by Oxford Nanopore (2 mentions) Ampure xp bead, by Beckman Coulter (2 mentions) Hiseq 2500, by Illumina (1 mentions) Nextera xt dna library preparation protocol, by Illumina (1 mentions) Genfind v3, by Beckman Coulter (1 mentions) Magna pure 96 system, by Roche (1 mentions) R9.4 flow cell, by Oxford Nanopore (1 mentions) 1d genomic dna sequencing kit sqk lsk108, by Oxford Nanopore (1 mentions) Ligation sequencing kit, by Oxford Nanopore (1 mentions) Sanger sequencing, by Eurofins (1 mentions) Ligation sequencing kit sqk lsk108, by Oxford Nanopore (1 mentions) Minion platform, by Oxford Nanopore (1 mentions) Qubit 3.0 fluorimeter, by Thermo Fisher Scientific (1 mentions) Q5 high fidelity dna polymerase, by New England Biolabs (1 mentions) Protoscript 2 first strand cdna synthesis kit, by New England Biolabs (1 mentions)

Close spelling variants of this product

Native Barcoding Kit (20 citations) EXP-NBD103 (17 citations)

4 protocols using native barcoding kit exp nbd103

Closed Bacterial Genomes via Short- and Long-Read Sequencing

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DNA was extracted using the MagNAPure 96 system (Roche Applied Science, Manheim, Germany) and sequencing libraries were prepared using Nextera XT DNA Library preparation protocol (Illumina, San Diego, CA, USA). Paired-end reads (2 × 150, 2 × 250 or 2 × 300 bp) were generated for all isolates using Illumina MiSeq with v3 chemistry. For isolates where only FASTQ files were received, sequencing was performed on an Illumina HiSeq 2500 at Eurofins Genomics (Eurofins Genomics Europe, Konstanz, Germany) generating 2 × 125 bp paired-end reads.
To achieve closed genomes, selected isolates were also long-read sequenced. DNA was extracted manually using the Beckman Coulter Life Science GenFind v3 kit (C34881) according to the supplemental protocol ‘DNA extraction from Bacteria using GenFind v3’ (Beckman Coulter, Brea, CA, USA). DNA libraries were prepared using the 1D Ligation sequencing kit (SQK-LSK108) and the Native barcoding kit (EXP-NBD103) [Oxford Nanopore Technologies (ONT), Oxford, UK] according to the ONT protocol ‘native barcoding genomic DNA’ or ‘genomic DNA by ligation’ without shearing to maximize the sequencing read length. Finally, libraries were loaded onto a R9.4.1 MinION flow cell (FLO-MIN106) or a R9.4.1 Flongle flow cell (FLO-FLG001) and sequenced on an ONT MinION Mk1B device (MIN-101B).

Fostervold A., Hetland M.A., Bakksjø R., Bernhoff E., Holt K.E., Samuelsen Ø., Simonsen G.S., Sundsfjord A., Wyres K.L, & Löhr I.H. (2021). A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001–15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. Journal of Antimicrobial Chemotherapy, 77(3), 665-674.

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Nanopore Sequencing of Amplicons

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We sequenced amplicons from 4 UR and 15 INS samples using the Oxford Nanopore MinION (Oxford Nanopore Technologies, Oxford, UK) according to the protocol described in Quick et al. [20 (link)]. Amplicons were barcoded using the Native Barcoding Kit EXP-NBD103 (Oxford Nanopore Technologies, Oxford, UK) and pooled in equimolar fashion. Sequencing libraries were prepared using the 1D Genomic DNA Sequencing kit SQK-LSK108 (Oxford Nanopore Technologies, Oxford, UK). We used AMPure XP beads (Beckman Coulter, Brea, CA, USA) for all purification steps performed as part of library preparation. Prepared libraries were sequenced on R9.4 flowcells (Oxford Nanopore Technologies, Oxford, UK) at the INS in Bogotá and at the Fred Hutchinson Cancer Research Center in Seattle.

Black A., Moncla L.H., Laiton-Donato K., Potter B., Pardo L., Rico A., Tovar C., Rojas D.P., Longini I.M., Halloran M.E., Peláez-Carvajal D., Ramírez J.D., Mercado-Reyes M, & Bedford T. (2019). Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC Infectious Diseases, 19, 963.

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Chromosomal Integration Verification of Myo5 Mutations

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Single chromosomal integration of the myosin mutagenesis-cassettes into the Myo5 locus was verified by long-read whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK). Briefly, the library was prepared from ~1000–2000 ng high-molecular weight (HMW) DNA according to the Ligation Sequencing Kit (SQK-LSK108 or SQK-LSK109 for the MinION and Promethion, respectively) and the Native Barcoding Kit (EXP-NBD103) (Oxford Nanopore Technologies, UK). The libraries were loaded onto primed Flo-min6 (R9.4 chemistry) or FLO-PRO002 (R9.4.1 chemistry) flow-cells and sequenced on the MinION or Promethion (Alfa/Beta) DNA sequencers (Oxford Nanopore Technologies, UK). Reads were base-called by Albacore v.2.0.1 and then trimmed and demultiplexed in Porechop v.0.2.3. The incorporation of the individual mutations was further verified by Sanger Sequencing (Eurofins Genomics, Germany) of PCR products spanning the relevant codons. All primers are listed in S1 Table in S1 File.

Wollenberg R.D., Donau S.S., Taft M.H., Balázs Z., Giese S., Thiel C., Sørensen J.L., Nielsen T.T., Giese H., Manstein D.J., Wimmer R, & Sondergaard T.E. (2020). Undefeated—Changing the phenamacril scaffold is not enough to beat resistant Fusarium. PLoS ONE, 15(6), e0235568.

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Zika Virus Genome Sequencing Protocol

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A protocol developed by Quick and collaborators [24 (link)] was used. The cDNA synthesis was generated using the ProtoScript II First Strand cDNA Synthesis Kit (New England Biolabs, Hitchin, UK) and random hexamer priming. The cDNA generated was subjected to multiplex PCR using Q5 High-Fidelity DNA polymerase (New England Biolabs, UK) and a set of specific primers (ZikaAsian V2) designed by the ZiBRA project (https://github.com/zibraproject/zika-pipeline, accessed on 29 September 2022). Amplicons were purified using 1× AMPure XP beads (Beckman Coulter, High Wycombe, UK) and quantified on a Qubit 3.0 fluorimeter (Life Technologies, Carlsbad, CA, USA) using the Qubit dsDNA BR assay. Library preparation was performed using the Ligation Sequencing Kit SQK-LSK108 (Oxford Nanopore Technologies, Oxford, UK) and Native Barcoding Kit EXP-NBD103 (Oxford Nanopore Technologies, UK). Sequencing libraries were loaded into an R9.4/R9.4.1 flow cell (Oxford Nanopore Technologies, UK), and sequencing data were collected for up to 48 h on a MinION platform (Oxford Nanopore Technologies, UK).

de Moraes L., Portilho M.M., Vrancken B., Van den Broeck F., Santos L.A., Cucco M., Tauro L.B., Kikuti M., Silva M.M., Campos G.S., Reis M.G., Barral A., Barral-Netto M., Boaventura V.S., Vandamme A.M., Theys K., Lemey P., Ribeiro G.S, & Khouri R. (2023). Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. Viruses, 15(6), 1236.

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