RNA-seq of M. smegmatis when exposed to new quinoxaline 1,4-dioxide derivative
Cells from 10 ml culture were  by centrifugation for 10 min at 3000g and 4C, washed twice by 10 ml of fresh Middlebrook 7H9 broth to remove the traces of 3a and DMSO and once by 3 ml of RNAprotect Bacteria Reagent (Qiagen, United States) for RNA stabilization. M. smegmatis cells were homogenized in ExtractRNA reagent (Evrogen, Russia), followed by phenol (pH = 4.5)-chloroform-isoamyl alcohol (25:24:1) purification and precipitation with isopropanol (2:1, v/v). DNase treatment was carried out as previ-ously described [18] with TURBO DNA-free kit (Thermo Fisher Scientific, Waltham, MA, United States), in volumes of 100 ml, and further with the RNase-Free DNase Set (Qiagen, Hilden, Germany), according to the manufacturers protocol. RNA cleanup was per-formed with the RNeasy Mini Kit (Qiagen). The concentration and quality of the total RNA were checked by the Quant-iT RiboGreen RNA assay (Thermo Fisher Scientific, United States) and the RNA 6000 Pico chip (Agilent Technologies, Santa Clara, CA, United States), respectively.