RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

We aimed to illuminate the effects on the transcriptome upon translation knockdown (KD) of core genes and other characterised genes or early expressed genes in PHIKZ through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle. The read coverage can point to alterations in transcripts and mode of action for several candidates that were knocked down. Overall design: PAO1 cells were pretreated with anti-sense-based molecules against the start codon and ribosome binding site of PHIKZ transcripts. Cells were infected with PhiKZ and at defined time-points post-infection, cells were harvested. RNA was extracted from cells and sequenced.