Extended Data Fig. 6: Early-middle/late gene classification and effects upon inhibition of ChmA synthesis.
From: Programmable antisense oligomers for phage functional genomics
a. Log2FC in transcript levels based on RPKM counts 35 vs. 10 min post infection in the samples treated with a non-targeting control ASO. Phage genes were classified as early (blue) upon depletion, and as middle/late (red) upon enrichment in the Log2FC plot 35 vs. 10 min. Other phage transcripts remained unaltered in the comparison of these two time points and were likely transcribed by the vRNAP. Two independent replicates were merged by geometrical averaging and the p-values were calculated by the Wald test (two-sided) without adjustments for multiple comparisons using DESeq2. b. PAO1 cells were pretreated with 6 µM ASO against chmA. Cells were infected with ΦKZ at an MOI = 5 and incubated for the indicated times followed by RNA extraction and sequencing of the transcriptomes. Relative quantification of protein-coding transcript (CDS) reads to total reads (RPKM) is shown. c. Relative read counts to total counts for phage tRNAs in the tRNA fraction in the samples treated with the non-targeting control ASO and the ASO targeting chmA; results are depicted as an overlay of two independent experiments. d. Transcript levels in samples treated with a non-targeting control ASO or an ASO targeting chmA were normalized over the course of infection and clustered by t-SNE. Individual clusters are represented together with genomic locations, core genes and blocks. Source data for panel (a) are available online.
