title: Resequencing of Neisseria gonorrhoeae: parental and compensatory mutants isolated from the experimental mouse model of infection
design: Genomic DNA was extracted using the Promega Wizard Genomic DNA purification kit (Promega, Madison, WI) according to the manufacturer's protocol using bacteria grown to mid-log phase in supplemented GC broth. The extracted DNA was rehydrated overnight, and a mate-pair library was constructed using Nextera XT standard kits (Illumina FC-121-1024 and FC-121-1001) and prepared for emulsion-based amplification and paired-end sequencing. Illumina MiSeq 2500 Genomic DNA paired-end sequencing was conducted by the Tufts University Core Facility using a v2 flow cell paired-end 250 base format. Each read was 251 bases with two reads per insert plus a barcode. The insert for PE250 with Nextera XT ranges from 500 bp to 1300 bp, with the average/peak size range around 800 bp. Data were aligned to the recently sequenced FA19 genome sequence using CLC Genomics Workbench version 6.0.4.