RNA seq of PhiKZ
Samples were collected at 40 mpi in the stop buffer (phenol:ethanol 5%:95%). Snap-frozen in liquid nitrogen and stored in -20C. Cells were pelleted at 3000 rpm in a swinging bucket rotor, the pellet washed with 1x DPBS (Millipore Sigma D4031-1L), then RNA was isolated using an RNA isolation kit (New England Biolabs T2010). The integrity and quality of RNA was analyzed using Agilent TapeStation 4150. For library preparation, 1 g of total RNA was used. The rRNA was removed and remaining RNA was purified using magnetic beads (New England Biolabs E7860L). The cDNA was synthesized and libraries were prepared (New England Biolabs E7770S, New England Biolabs E7600S). The samples were sequenced using Nova-Seq 6000 illumina platform  and >20 million of 50 base pair (bp) paired-end reads were collected per sample. The quality of reads were determined using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads with greater than Q30 values were selected for further analysis.