Analyzing the impact of antibiotics treatment on lung inflammation in Mtb infected mouse lungs using bulk RNA transcriptomics

C3HeB/FeJ mice were infected with Erdman strain of Mycobacterium tuberculosis (Mtb) for 12 weeks. Mice were then treated with RIPE (rifampin, isoniazid, pyrazinamide, and ethambutol) or carrier (water). Lungs were harvested after 2, 4, and 8 weeks of treatment (times 14, 16, and 20 weeks post0infection) for RNA preparation and bulk RNA sequencing. Overall design: Uninfected, infected/carrier-treated and infected/RIPE-treated mouse lungs were soaked in RNAlater and frozen at -80; RNA was then isolated using Trizol (Invitrogen) according to the manufacturer's protocols. RNAseq libraries were generated, sequenced, and analyzed