Active Mycobacterium tuberculosis regulatory networks from in vitro infection of mouse macrophages uncovered by Path-seq

Transcriptional profiling of Mycobacterium tuberculosis mRNA enriched from host-pathogen samples from in vitro bone marrow derived macrophages (Mus musculus). Overall design: Mouse bone marrow derived macrophages (BMDMs) were infected with MTB H37Rv strain (MOI 10), followed by washing 3x with RPMI at 2 h post infection. At 2 h, 8 h, and 24 h MTB infected BMDMs were lysed with TRIzol (Invitrogen) and total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media and uninfected BMDMs were also collected at the same time points. Samples were either processed by Path-seq, RNA-seq or and profiled by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned to a combined M. tuberculosis and M. musuclus genome with Bowtie2 and processed using the R package DuffyNGS.