Hi-GRIL-Seq of lytic phage ICP1 infection of V. cholerae containing phage satellites

Vibrio cholerae containing the phage inducible chromosomal island-like element (PLE) were infected with the lytic Vibrio cholerae phage ICP1. ICP1 infection triggers transcriptional activation of PLE, which we leverage here to study the RNA-RNA interactome of ICP1 and PLE. Hi-GRIL-seq was carried out in the system, leading to in vivo ligation of interacting transcripts which were subsequently isolated and sequenced with paired end 150x150 RNAseq, allowing for identification of interacting transcripts during ICP1 infection.