GSM7698586: Gentamicin, 60 min, 3'-end-seq, Δmfd; Escherichia coli BW25113; RNA-Seq
For RNA exactraction, bacteria lysate was prepared using lysozyme and proteinase K. Total RNA was then purified by RNAClean XP beads (Beckman, A63987). For genomic DNA, TIANamp Bacteria DNA kit (TIANGEN, DP302) were used. See decrisption in our paper for details. 3' -end-seq library preparation method was adopted from a previous multiplexed RNA-seq library preparation method reported by Avraham et al. Systematic modifications were introduced to repurpose it to keep 3' end information of bacterial transcripts. To prepare RNA-seq library, here we did not follow routine RNA-seq library construction method, in order to minimize the batch effect introduced when applying different library preparation protocols.