Expression profiling by high throughput sequencing.

S. aureus JE2 wild-type (WT) or its isogenic JE2 brnQ1 mutant were either used to infect primary human macrophages for 10h or were cultivated in Infection Medium (RPMI1640 + 10% v/v heat-inactivated FBS) for 10h. RNA of both pathogen and host cells were isolated together (dual RNA-Seq of infected macrophages) or isolated from planktonic bacteria (Infection Medium) after 10h of infection/cultivation. DESeq2 was used to analyse the following conditions: host transcripts in human macrophages infected with JE2 brnQ1 compared to infected with JE2 WT (HUMAN-ic_Mut_vs_ic_WT); bacterial transcripts for intracellular JE2 brnQ1 compared to intracellular JE2 WT (BACT-ic-Mut_vs_ic_WT); bacterial transcripts in intracellular bacteria compared to Infection Medium for JE2 brnQ1 (BACT-ic_Mut_vs_RPMI_Mut) or JE2 WT (BACT-ic_Mut_vs_RPMI_WT) (HUMAN: human transcripts; BACT: bacterial transcripts; Mut: JE2 brnQ1; WT: JE2 WT; ic: intracellular; RPMI: Infection Medium).
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