title: RNA-seq of Mycobacterium tuberculosis H37Rv treated with alpibectir or a combination of alpibectir and ethionamide against untreated controls
design: RNA-seq of Mycobacterium tuberculosis H37Rv treated with alpibectir or a combination of alpibectir and ethionamide against untreated controls
library_construction_protocol: 10 mL of the treated and control cultures were harvested by centrifugation at 3,000 x g for 5 min. 25 mL cultures were grown at 37°C without agitation to an optical density at 600 nm of 0.7.  Individual cultures at an optical density of 0.7 were treated with alpibectir 0.1 mg/L alone for 24 h or with alpibectir 0.1 mg/L for 20 h followed by ethionamide 2 mg/L for 4 h at 37°C without agitation. The pellets were resuspended in 1 mL of RNAproTM (FastRNA Pro Blue Kit, MP biomedicals) and homogenized in impact-resistant 2 mL tubes containing 0.1 mm silica spheres (Lysing Matrix B, MP biomedicals) using a FastPrep FP120 cell disrupter (Thermo Fisher Scientific) at 6.0 Hz for 40 s. The ribolysed cells were centrifuged at 12,000 x g to remove cellular debris and RNA was purified following the manufacturer's instructions. Ribosomal RNA (rRNA) depletion was performed using QIAseq FastSelect –5S/16S/23S Kits; Qiagen). Libraries for Illumina sequencing were prepared with the TruSeq RNA sample preparation kit version 2.0 rev. A (Illumina Inc.). All cDNA libraries were uniquely indexed. 