Extended Data Fig. 4: Protospacer flanking site (PFS) sequences for DiCas7-11 and effect of accessory proteins on interference.

a, Gating strategy used for all bacterial RFP knockdown experiments in Fig. 1e, g and Extended Data Fig. 6l. b, Schematic for targeting of DiCas7-11 DNA target in a plasmid with resulting sequence motifs. c, Schematic for targeting of DiCas7-11 RNA target in β-lactamase (ampicillin resistance gene) and the resulting PFS determined by 20 depleted targets. d, PFS analysis of top spacers from the MS2 phage screen (e-5 condition) in the 8 bp flanking the target region to the left. e, PFS analysis of top spacers from the MS2 phage screen (e-5 condition) in the 8 bp flanking the target region to the right. f, Schematic of the Type III-E locus of the Desulfonema ishimotonii. g, Phage plaque assay of the Type III-E DiCas7-11 effector alone and as part of the entire locus. Two top MS2 targeting guides along with four non-targeting guides are used to assess target interference and survival against phage. Resistance is quantified as the highest surviving titer of MS2 phage that generates plaques in the dilution assay. h, Phage plaque assay of E. coli transformed with the DiCas7-11 locus containing corresponding accessory gene knockouts. A top MS2 targeting guide along with a non-targeting guide is used. Resistance is quantified as the highest surviving titer of MS2 phage that generates plaques in the dilution assay. Data are mean ± s.e.m.; n = 3. i, Phage plaque assay of E. coli transformed with either the complete DiCas7-11 locus or DiCas7-11 supplemented with corresponding accessory gene knock-ins. A top MS2 targeting guide along with a non-targeting guide is used to assess target interference and survival against phage. Resistance is quantified as the highest surviving titer of MS2 phage that generates plaques in the dilution assay. Data are mean ± s.e.m.; n = 3.