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RNA sequencing transcriptome analysis allows for the characterization of the infection gene expression profiles of pathogens in complex environments. Isolation of the pathogen from infected tissues is critical because of the large amounts of host RNA present in crude lysates of infected organs. A filtration method was developed that enabled enrichment of the pathogen RNA for RNA-seq analysis. The resulting data describe the \u201cinfection transcriptome\u201d of\n            <jats:named-content content-type=\"genus-species\">B. pertussis<\/jats:named-content>\n            in the murine lung. 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