Bulk RNAseq profiling of Streptococcus pneumoniae EF3030 and Influenza A virus (A/California/07/2009(H1N1)) mono/coinfection in the mouse lungs.

To investigate the host-pathogen interactions of Streptococcus pneumoniae EF3030 (NZ_CP035897) and Influenza A virus (A/California/07/2009(H1N1)) in the mouse lung. We generated monoinfections and coinfections of C57BL/6 mice, as well as mock infection controls, and harvested whole mouse lung homogenates. Overall design: We performed gene expression profiling analysis using bulk RNA-seq. K-means clustering of normalized gene expression values was used to identify true mock/coinfected cohorts of samples (mock infected, EF3030 infected, pH1N1 infected, and EF3030+pH1N1 coinfected), as some mice cleared infections over time. As such, with a focus on EF3030 infected and EF3030+pH1N1 coinfected groups, samples that did not fit into these 2 group clusters were labeled "inconclusive_infection".