RNA sequencing data of Mycobacterium marinum treated with compound 8
The mechanisms of action of compound 8 in Mycobacterium marinum although it inhibits the secretion of the bacteria. In this experiment, we aim to investigated the effect of compound 8 on the global gene expression of Mycobacterium marinum Overall design: M. marinum cells were grown treated with compund Compound 8-73 or DMSO  at 10 µM or 20 µM. Bacteria were harvested by centrifugation and flash frozen in liquid nitrogen. The RNA of biological duplicates was isolated using the NucleoSpin RNA kit (Macherey-Nagel). The bacteria were lysed by bead beating with zirconium beads in 500 µL buffer RA1 and 5 µL ß-mercaptoethanol for 1 min. The rRNA was depleted and mRNA was enriched using RiboMinus prokaryotic kit (Invitrogen). The mRNA was outsourced to BaseClear (Leiden, The Netherlands) for RNA sequencing analysis. Subsequently, low-quality reads were excluded and the remaining reads were aligned to M. marinum MUSA reference genome (NC_010612.1) by CLC Genomics Workbench 12. Count data were converted to reads per million (rpm) and differential analysis was performed using CLC Genomics Workbench 12 or independently analysed by BaseClear service. Gene function and classification were later determined with  mycobrowser (https://mycobrowser.epfl.ch/).