title: NextSeq 500 paired end sequencing; RIL-seq of EPEC E2348/69 hfq-flag,  in virulence activating and non-activating conditions.
design: RIL-seq of EPEC E2348/69 hfq-flag,  in virulence activating and non-activating conditions.
library_construction_protocol: EPEC E2348/69 hfq-Flag strain 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. in activating- conditions:growth on DMEM at 37°C to mid exponential growth phase (e.g., OD600=0.3). In these conditions EPEC strongly expresses its major virulence components, T3SS and BFP, mimicking infection RIL-seq experiments were performed as described in Melamed et al 2018, PMID: 29215635 , each repeated three times. RNAtag-Seq protocol (Shishkin et al., 2015)