Protocol for dual spatial transcriptomic profiling of infected tissues

Dual spatial transcriptomics analysis offers profiling of host- and pathogen-specific transcriptional patterns in infected tissues to establish pathoadaptation signatures and predict infection outcomes. Here, we present a protocol for tissue processing, imaging, selection of regions of interest, library preparation, sequencing, and analysis pipeline. This protocol has a potential application for the analysis of any infected tissue. For complete details on the use and execution of this protocol, please refer to Zhou et al. 1 • Maps host and pathogen transcripts in the same tissue sections • Works on FFPE slides with WTA and custom pathogen probes • Defines ROI by GeoMx and yields high-depth, high-quality libraries • Links host profiles to local bacterial burden using machine learning Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Dual spatial transcriptomics analysis offers profiling of host- and pathogen-specific transcriptional patterns in infected tissues to establish pathoadaptation signatures and predict infection outcomes. Here, we present a protocol for tissue processing, imaging, selection of regions of interest, library preparation, sequencing, and analysis pipeline. This protocol has a potential application for the analysis of any infected tissue.