Set up the Heme Biosensor ARC

studies/ALECloneScreening/protocols/WholeGenomeSequencing.md

+Whole genome sequencing (WGS) of isolated C. glutamicum clones was performed using next generation sequencing (NGS). First, genomic DNA was prepared using NucleoSpin microbial DNA kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s instructions. Concentrations of the purified genomic DNA were measured using Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA, United States) according to manufacturer’s instructions. The purified genomic DNA was used for the preparation for genome sequencing using NEBNext Ultra II DNA Library Kit for Illumina (New England BioLabs, Frankfurt am Main) and MiSeq Reagent Kit v2 (300-cycles) (Illumina, San Diego, CA, United States), according to manufacturer’s instructions. A MiSeq system (Illumina, San Diego, CA, United States) was used for sequencing. Data analysis and base calling were accomplished with the Illumina instrument software. FASTQ output files were analyzed for single nucleotide polymorphisms using BV-BRC web resources (3.34.11, https://www.bv-brc.org/) (Olson et al., 2023) via variation analysis and CLC Workbench 20.0.4 (https://digitalinsights.qiagen.com/) for structural variants and InDel analysis. 
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