High-depth RNA-seq data to investigate gene regulation mediated by phase-variable DNA methyltransferases in serogroup B <i>Neisseria meningitidis</i>

<i>Neisseria meningitidis</i> is a leading cause of bacterial meningitis and septicemia. Here, we report high-depth RNA-seq for <i>N. meningitidis</i> serogroup B strains MC58, B6116/77, and M0579. These strains encode phase-variable DNA methyltransferases ModA11, ModA12, and ModD1, respectively, which act as global epigenetic regulators central to meningococcal pathogenicity.