title: NextSeq 500 paired end sequencing; RNA-seq of EPEC E2348/69 in virulence activating and non-activating conditions. Comparison of wt and dhfq strains.
design: RNA-seq of EPEC E2348/69 in virulence activating and non-activating conditions. Comparison of wt and dhfq strains.
library_construction_protocol: EPEC E2348/69 w.t and delta-hfq strains was grown in 2 set of conditions: For non-activating conditions, the culture was grown overnight in LB, without shaking. For activating conditions, a non-activating culture was diluted 1:100 into Dulbecco's modified Eagle medium (DMEM, Biological Industries) and grown to reach OD600 of 0.3.  Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze at 37°C and in liquid nitrogen, respectively, and RNA was extracted using Tri-Reagent (Sigma Aldrich) RNAtag-Seq protocol (Shishkin et al., 2015)