Abstract
A detailed knowledge about virulence-relevant genes, as well as where and when they are expressed during the course of an infection is required to obtain a comprehensive understanding of the complex host-pathogen interactions. The development of unbiased probe-independent RNA sequencing (RNA-seq) approaches has dramatically changed transcriptomics. It allows simultaneous monitoring of genome-wide, infection-linked transcriptional alterations of the host tissue and colonizing pathogens. Here, we provide a detailed protocol for the preparation and analysis of lymphatic tissue infected with the mainly extracellularly growing pathogen Yersinia pseudotuberculosis. This method can be used as a powerful tool for the discovery of Yersinia-induced host responses, colonization and persistence strategies of the pathogen, and underlying regulatory processes. Furthermore, we describe computational methods with which we analyzed obtained datasets.
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