RNA-Seq of Mycobacterium smegmatis
Total RNA was isolated from all M. smegmatis cultures. DNase treatment was carried out with TURBO DNA-free kit (Thermo Fisher Scientic, Waltham, USA) in volumes of 100 L and further with the RNase-Free DNase Set (Qiagen, Hilden, Germany) according to the manufacturers protocol. RNA cleanup was performed with the RNeasy Mini Kit (Qiagen) and the resultant RNA was stored at 70oC until further use. The concentration and quality of the total RNA were checked by the Quant-it RiboGreen RNA assay (Thermo Fisher Scientic) and the RNA 6000 pico chip (Agilent Technologies, California, USA), respectively. Total RNA (1 - 2.5 g) was used for library preparation as previously described [Julia Bespyatykh, et al. Pathogens, 2020]. Equimolar quantities of all libraries (12 pM) were sequenced by a high throughput run on the Illumina HiSeq2500 using 2  100 bp paired-end reads and a 5% Phix spike-in control