RNA-seq of MRA_3376 mutant 3
Mycobacterial strain was grown in 7H9 to mid logarithmic phase and were collected by centrifugation. Total RNA was extracted using an RNeasy mini kit (Qiagen, Germany). Library constructions were prepared using TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) and RNA sequencing was conducted using an Illumina HiSeq2500 (Illumina, USA) at Shanghai Biotechnology Corporation. The inser size conformation of purified libraries was validated by an Agilent 2100 bioanalyzer (Agilent Technologies, USA). Bowtie2 v2-2.0.5 was used to map the cleaned reads to the M. tuberculosis H37Ra genome acquired from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/nuccore/CP000611.1). Then, HTSeqv2.1.1 was run with a reference annotation to generate fragments per kilobase of exon model per million mapped reads values for estimation of fold-changes. Three biological replicates were used in RNA-seq and the p- and q-values were calculated. The differentially expressed genes were selected using the following filter criteria: the false discovery rate FDR  0.05 and fold-change  1.5.