Transcriptome Analysis of Staphylococcus aureus

Overnight culture in TSB was diluted 100 times in a fresh TSB and incubated in a shaking incubator at 37 °C for 8 h. After immediate stabilization of RNA in all samples by RNAprotect Bacteria Reagent (Qiagen), cells were collected by centrifugation, suspended in TE buffer (10 mM Tris HCl, pH 8.0, 1 mM EDTA) and treated with lysostaphin (50 µg/mL final concentration) at 37 °C for 10 min. From the lysed cells, total RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. The isolated RNA was sent to the Center for Genomics and Bioinformatics at Indiana University. Sequencing libraries were constructed using the ScriptSeq Complete Kit for Bacteria (Epicentre). The statistical analysis of the RNA-seq results was done with DeSeq. 2 as described previously^{49 (link)}. The RNA-seq results were deposited in GEO (Gene Expression Omnibus) with the accession number GSE89791.