PT  - JOURNAL ARTICLE
AU  - James W. Marsh
AU  - Regan Hayward
AU  - Amol Shetty
AU  - Anup Mahurkar
AU  - Michael S. Humphrys
AU  - Garry S. A. Myers
TI  - Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells
AID  - 10.1101/098715
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 098715
4099  - http://biorxiv.org/content/early/2017/01/06/098715.short
4100  - http://biorxiv.org/content/early/2017/01/06/098715.full
AB  - Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest.