CLIP-seq of Salmonella ProQ in intracellular-like conditions

The aim of the project is to identify transcriptome-wide binding sites for the global RNA-binding protein ProQ in Salmonella during intracellular-like conditions. Overall design: Salmonella enterica strain SL1344 carrying a chromosomal proQ-3xFLAG allele was grown in intracellular-like growth medium until and OD600 of 0.3 and thereafter subjected to crosslinking immunoprecipitation sequencing (CLIP-seq). Specifically, the bacteria were subjected to UV-light-induced crosslinking, anti-FLAG-mediated immunoprecipitation, RNase treatment, gel purification, and RNA purification, followed by Illumina library preparation using the NEBNext Small RNA Prep kit and sequencing on an Illumina NextSeq500 instrument at vertis Biotechnologie AG (Freising, Germany).