RNA-Seq of Mycobacterium tuberculosis: in vitro resuscitation
RNA was isolated using phenol-chloroform extraction and cell disruption with BeadBeater (BioSpec Products). RNA was treated with Turbo DNase (Life Technologies) to remove traces of genomic DNA, and purified with the RNeasy mini kit (Qiagen, Venlo, Netherlands). RNA samples were depleted of 16S and 23S rRNA with Ribo-Zero (Epidemiology) (Illumina). Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina) (Samples dorm1_run1, dorm2_run1, dorm3_run1, day1_1, day1_2, day1_3, day2_1, day2_2, day2_3, day4_1, day4_2, day4_3) or NEBNext Ultra II Directional RNA (NEB) (Samples dorm1_run2, dorm2_run2, dorm3_run2, day7_1, day7_2, day7_3).