Transcriptomic data of log-phase Mycobacterium tuberculosis (Mtb) exposed to MALF and rcBALF
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.  After trimming the adaptors with cutadapt (version1.18)( https://cutadapt.readthedocs.io/en/v1.18/), RNA reads were aligned and mapped to the Mycobacterium tuberculosis genome (H37Rv) by Bowtie 2 version 2.2.8 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml. Raw read counts per gene were extracted using HTSeq-count v0.11.2.ene expression profiles were constructed for differential expression, cluster, and principle component analyses with the DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter.  Corrected p-values were calculated based on the Benjamini-Hochberg method to adjusted for multiple testing.