RIL-seq on CsrA RNA binding protein in EPEC bacteria
To elucidate the regulatory network of CsrA in infecting EPEC and identify the single and possibly two distinct RNA molecules bound to CsrA, we employed the RIL-seq methodology (Melamed et al., 2018; Melamed et al., 2016). EPEC expressing FLAG-tagged CsrA (NN6861) was cultured in DMEM under conditions known to activate its virulence machinery, while wild type EPEC expressing an untagged CsrA served as the negative control. The RIL-seq experiment was performed following Melamed et al. (Melamed et al., 2018), with minor modifications, in six biological replicates