GSM9543832: Salmonella Typhimurium Δpimt, mid log, biol rep 1; Salmonella enterica subsp. enterica serovar Typhimurium; RNA-Seq
Frozen bacterial pellets were subjected to RNA extraction using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions. RNA was quantified using a Qubit fluorometer, and RNA integrity was assessed using High Sensitivity RNA ScreenTape to determine RIN values. 1000 ng of RNA sample was used for ribodepletion by using NEBNext rRNA depletion kit Bacteria (Cat. no. NEB E7850X). The NEBNextâ Ultra II Directional RNA Library prep kit for Illumina (Cat. no. E7760L) was used to construct double-stranded cDNA libraries from the rRNA-depleted RNA, using RNA fragmentation. First strand cDNA synthesis with random primers, second strand cDNA synthesis, end repair of double-stranded cDNA, adapter ligation, removal of excess adapter using sample purification beads, PCR enrichment of adapter-ligated DNA and clean-up of PCR products were done as instructed by the manufacturer's protocol. The cleaned libraries were quantified on a Qubit fluorometer, and appropriate dilutions were loaded on a D1000 screen tape to determine the size range of the fragments and the average library size.