title: Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions
design: Whole genome sequencing was performed on cultured S. epidermidis isolates to provide genomic context for downstream RNA-sequencing analyses. Genomic DNA of the 19 S. epidermidis isolates was extracted using previously described methods (27). DNA was extracted using the Zymo Research Quick-DNA Fungal/Bacterial Miniprep kit (Zymo Research, Irvine, CA, US) and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Approximately 0.5 mg of DNA was prepared for DNA libraries using a Nextera XT PE kit (Illumina, San Diego, CA, US). Whole genome sequencing was performed on an Illumina HiSeq 4000 with a 2 x 150-bp setting and 60 sample libraries multiplexed per flow cell.