GSE175812
Transcriptomic changes associated with growth of Mycobacterium tuberculosis H37Rv wild-type strain and ?prpR mutant in mineral medium supplemented with cholesterol as the sole carbon source or standard medium supplemented with vitamin B12.
RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis  ?prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in  three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12. The study allowed us to re-establish the list of genes potentially involved in cholesterol metabolism. We further proposed a novel regulatory function of vitamin B12 and PrpR, a propionate regulator, in coordinated cholesterol breakdown metabolite dissipation and virulent phenotype induction. Finally, we demonstrated that a key role of cholesterol in Mtb metabolism is not only providing carbon and energy but also inducing a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment. Overall design: Next generation sequencing results are provided in  three independent biological replicates for each strain growing in three different media - minimal medium with 0.1% glycerol (vol/vol), minimal medium with 0.01% cholesterol (wt/vol) and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12 (10 µg/ml). For DGE analysis of bacteria grown in mineral medium with cholesterol, results obtained in medium with glycerol were treated as reference. For better specificity, the expression data for mineral medium with cholesterol were compared to the data obtained on standard  7H9/10% OADC medium. Only genes that were differentially expressed on cholesterol but NOT on 7H9/10% OADC were included to further studies and discussion. For the study on the role of vitamin B12 in shaping M. tuberculosis transcriptome the RNA-Seq analysis of the M. tuberculosis growing in 7H9/10% OADC medium supplemented with vitamine B12 was compared to the results obtained for M. tuberculosis growing in 7H9/10% OADC medium without B12 (reference).