Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions
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.