Project description:In order to identify genes that were differentally regulated upon oral infection with EPEC, we isolated 8 days post-infection intestinal epithelial cells (IECs) from the small intestine of C57BL/6 neonate mice that were left untreated or orally infected with 5x104 WT EPEC E2348/69 or with 5x104 of the isogenic mutant ΔescV on their first day of life.
Project description:Compared the transcriptome of wild type EPEC with that of an isogenic Δhfq mutant. Comparing 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. Non-activating conditions: overnight growth of static culture on LB medium at 37°C where virulence factors are not expressed.
Project description:RIL-seq experiment of EPEC hfq-flag mutant, 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. Non-activating conditions: overnight growth of static culture on LB medium at 37°C where virulence factors are not expressed. RIL-seq experiments are designed to reveal the interactions of sRNA and their targets.
Project description:The RNA content of the CsrA foci. EPEC (E2348/69 (strain O127:H6)) expressing CsrA-FLAGx3-GFP or wild-type EPEC expressing untagged CsrA (negative control) were grown to OD 0.6 in DMEM and subjected to the foci-enrichment protocol, followed by RNA extraction and library preparation. Six libraries were prepared, containing three biological repeats of csrA-3 x flag-gfp and three repeats of wt.
Project description:EPEC wild type E2348/69 (strain O127:H6) bacteria were grown overnight (ON) in LB medium (Sigma-Aldrich) at 37°C without shaking, diluted 1:40 into DMEM-HEPES (Gibco, Israel) medium and incubated for 3h at 37°C without shaking to exponential phase (optical density (OD) ~ 0.6). Bacteria were plated on LB plate with streptomycin (50 µg/ml), incubated at 32°C for 15h (for aerobic LB) or for 12h (for aerobic butyrate and infant stool metabolites conditions) or at 37°C (for anaerobic condition) for 12 h and colonies of two sizes (Virulent & Avirulent) were sampled, RNA was extracted and sequencing libraries were constructed based on the RNAtag-Seq protocol (Shishkin et al., 2015) with several modifications.
Project description:Global transcriptional analysis of the EPEC prototype strain E2348/69 and its plasmid mutants containing a deletion of perABC, or missing the entire EAF plasmid (strain JPN15).
