Non-canonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9 [RIP-seq]

RIP-seq analysis to identify CjCas9 bound RNAs using co-immunoprecipitation and sequencing in CG84-21. Overall design: Cas9 was chromosomally tagged using 3xFLAG epitope at the C-terminus in Campylobacter jejuni CG84-21 wild-type cells and immunoprecipitated using anti-FLAG antibody, untagged version of the wild-type CG84-21 strain was used as a control. Lysates for immunoprecipitation for both untagged and Cas9-3xFLAG samples were prepared from 60 O.D. of bacteria grown to mid-log phase ( OD600 ˜ 0.6) . RNA was eluted from both untagged and Cas9-3xFLAG samples to use for cDNA library preparation and sequencing.