RNA-seq PHIKZ-infected cells - early infection

The 280-kB giant bacteriophage PHIKZ expresses hundreds of transcripts upon infection of Pseudomonas aeruginosa. To illuminate which transcripts are the very first and abundant ones, we extracted RNA after infection and sequenced the transcripts. The early expressed genes promise to be important for surpassing the host defence systems and to reprogram the host machinery towards phage replication. We discovered a number of transcripts that encode for proteins which we found in an independent study to be associated with large complexes. In essence, early genes represent exciting opportunities to filter for important factors that could also engage in large complexes. Overall design: Pseudomonas aeruginosa PAO1 was grown in M9 minimal media with 0.4% glucose. Exponentially growing cells were infected at an MOI of 15 with PHIKZ in two replicates. At time points -2, 0, 2, 4, 6, 8, 10 min, we extracted RNA with hot phenol and sequenced the samples.