RNA-Seq PA14 A549

Cells were seeded in 6-well plates and incubated at 37 °C and 5 % CO2 overnight. The next day, cells were washed with 1X PBS, treated with BMVs and incubated at 37 °C and 5 % CO2 for 24 h. RNA isolation was performed by using the NucleoSpin® RNA kit (MACHEREY-NAGEL, 740955.50). cDNA synthesis was performed and libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina at the Genome Analytics at Helmholtz Centre for Infection Research. Libraries were sequenced using a NovaSeq 6000 instrument (Illumina) generating 50-bp reads in paired-end mode. Reads mapping and differential expression analysis were performed using the galaxy platform (https://usegalaxy.org/). Reads were mapped to the human genome hg19 with Hisat2 [2]. EdgeR was used to identify differential expression and calculate the P values with an exact test based on the dispersion generated by the quantile-adjusted conditional maximum likelihood (qCML) method.