Extended Data Fig. 7: ASO-mediated silencing of top hits has effects on host and phage transcript levels.
From: Programmable antisense oligomers for phage functional genomics
PAO1 cells were pretreated with 6 µM ASO against the 56 top hits for 30 min. Cells were infected with ΦKZ at an MOI = 5 and incubated for 15 or 30 min followed by RNA extraction, sequencing of the transcriptomes, and quantification of fold-change compared to the non-targeting control ASO. a., c. Heatmap for Log2FC for ΦKZ transcripts at 15 min (a) and 30 min (c) p.i. d., f. Heatmap for Log2FC for PAO1 transcripts at 15 min (d) and 30 min (f) p.i. b., e., g. t-SNE clustering of the log2fold change (Log2FC) of transcript levels of ΦKZ 15 min (b) or of PAO1 15 min (e) and 30 min (g) p.i. Phage proteins whose knockdown led to a strong phenotype (+++) in the CFU/PFU assay (in Supplementary Table 1) are labelled. h. Read coverage of the Pf4 prophage locus in PAO1 upon knockdown of ΦKZ082.
