Dual RNA-seq on pneumococcal infection to murine lung

Tropism is a very important factor in pneumococcal infection. Previous study has shown that clinical isolate showed niche preference in model organism. In particular, ear isolate showed particular tropism in nasopharyngeal carriage while blood isolate survives better in the murine lung. We have detected a SNP located inside rafR, repressor of sugar metabolism regulon, that contributes to strain tropism. We then perform a swap mutation between the rafR ear and blood isolates and perform intranasal infection using the four strains: original ear and blood isolates, ear isolate with rafR blood isolate and blood isolate with rafR ear isolate. We harvested the lung six hours into infection and exploited the recently described dual RNA-seq to reconstruct transcriptomics landscape during host-pathogen interaction. Overall design: Twelve samples are analysed, categorized into four conditions with three replicates each