Tissue dual RNA-seq: a fast discovery path for infection-specific functions and riboregulators shaping host-pathogen transcriptomes.

In this study we performed strand-specific RNA-seq of Yersinia pseudotuberculosis IP32953 grown under 4 different laboratory conditions (LB broth, exponential/stationary phase, 25C/37C), in biological triplicates. The first replicate is also available as a non TAP version to allow for bacterial transcriptional start site mapping. In addition, we performed Tissue dual RNA-seq of Yersinia pseudotuberculosis IP32953 within murine Peyer’s Patches (female BALB/c mice) and Peyer’s Patches of uninfected mice, in biological triplicates. ERCC ExFold RNA Spike-In Mixes were added to mouse rRNA depleted RNA from Peyer’s Patches. Raw FASTQ files are deposited under accession PRJEB14242. Here, we additionally provide cleaned FASTQ files as well as cleaned and pooled FASTQ files from dual RNA-seq technical duplicates. Moreover, we provide corresponding BAM files to allow visualization of the RNA-seq data in a genome browser.