title: Transcriptomic data of log-phase Mycobacterium tuberculosis (Mtb) exposed to MALF and rcBALF
design: 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.