Library preparation and sequencing were performed by MR DNA–Molecular Research LP, (Shallowater, TX, USA). In this process, 50 ng genomic DNA was used to prepare the libraries with the Nextera DNA Flex preparation kit (Illumina, San Diego, CA, USA) following the manufacturer’s user guide. The samples underwent simultaneous fragmentation and addition of adapter sequences. Libraries were pooled and diluted (to 0.6 nM), and 2 × 150 paired-end sequencing was performed on the NovaSeq system (Illumina, San Diego, CA, USA). Metagenomic sequence data from the 4 depths are available through NCBI at BioProject PRJNA688760
Nextera dna flex preparation kit
Manufactured by Illumina
Sourced in United States
The Nextera DNA Flex Preparation Kit is a laboratory equipment product designed for sample preparation. It enables the preparation of DNA samples for sequencing applications.
Automatically generated - may contain errors
Lab products found in correlation
Qubit fluorometer, by Thermo Fisher Scientific (4 mentions)
Novaseq system, by Illumina (1 mentions)
Plant fungi dna isolation kit, by Norgen Biotek (1 mentions)
Nextera dna flex, by Illumina (1 mentions)
Nextseq 1000 2000, by Illumina (1 mentions)
Rapid pcr barcoding kit sqk rpb004, by Oxford Nanopore (1 mentions)
Dneasy blood and tissue kit, by Qiagen (1 mentions)
Miseq platform, by Illumina (1 mentions)
3 protocols using nextera dna flex preparation kit
1
Metagenomic Sequencing of Environmental Samples
2
High-Throughput Genomic DNA Extraction
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The genomic DNA from the cultured isolates was extracted using the Plant/Fungi DNA Isolation Kit (Norgen Biotek CORP, Thorold, ON, Canada). The DNA samples were quantified using a Qubit fluorometer (ThermoFisher Scientific, Waltham, MA, USA) using a dsDNA High Sensitivity Assay. The sequencing libraries were prepared using the Nextera DNA Flex Preparation Kit (Illumina, San Diego, CA, USA) adopted from a previous study [10 (link)].
3
Genotyping of Bacterial Isolates
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All isolates were subcultured before DNA extraction. DNA was extracted using the Qiagen DNeasy Blood and Tissue kit (Qiagen, USA). Extracted samples were quantified using a Qubit fluorometer (ThermoFisher Scientific) using a dsDNA high-sensitivity assay. Sequencing libraries were prepared using the Nextera DNA Flex preparation kit (Illumina, USA). Library preparation protocol was adopted from the CDC PulseNet Nextera DNA Flex Standard operating protocol and sequenced using the Illumina Miseq platform and Nextseq 1000/2000 at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Nigeria.
To improve the plasmid assembly, we performed a single run on a GridION x5 to generate long reads. Library preparation and sequencing were done using the Rapid PCR Barcoding kit (SQK-RPB004) (Oxford Nanopore Technologies, Oxford, UK), following the manufacturer’s recommendations. We used a GridION MK1 sequencer, FLO-MIN106D R9 flow cell, and MinKNOW software v22.10.7 for sequencing.
To improve the plasmid assembly, we performed a single run on a GridION x5 to generate long reads. Library preparation and sequencing were done using the Rapid PCR Barcoding kit (SQK-RPB004) (Oxford Nanopore Technologies, Oxford, UK), following the manufacturer’s recommendations. We used a GridION MK1 sequencer, FLO-MIN106D R9 flow cell, and MinKNOW software v22.10.7 for sequencing.
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