Transcriptional response in RAW 264.7 macrophages infected with zinc-replete and zinc-limited Mycobacterium tuberculosis

The goal of this experiment was to determine if macrophages can distinguish between M. tuberculosis grown in standard, zinc-replete media and those grown in zinc-limited media. In order to determine this, we performed RNA-sequencing (RNA-seq) of RAW 264.7 macrophages infected with zinc-limited Mtb and zinc-replete Mtb at 4 hours post-infection (hpi) and 24hpi. Transcriptional response in the infected macrophages was compared to uninfected controls (macrophages exposed to growth media alone) and between macrophages infected with zinc-limited Mtb and zinc-replete Mtb at each time point. RNA was extracted and analyzed from 24 different samples: RAW 264.7 macrophages infected with zinc-replete and zinc-limited M. tuberculosis, and uninfected macrophage controls (added zinc-replete and zinc-limited media without bacteria) after 4 hours and 24 hours of infection, all in biological triplicates.