Extended Data Fig. 9: PRO-seq traces capture transcription of E. coli small regulatory RNAs.
From: Precision run-on sequencing (PRO-seq) for microbiome transcriptomics
(a) Normalized transcriptome profiles at selected E. coli small non-coding RNA (sRNA) loci. The left panel shows genomic context 2 kb up- and downstream from each sRNA locus (small black arrow). On the right, RNAseq coverage, composite PRO-seq read coverage, 5’ end and 3’ end coverage are shown for the sRNA locus, the bounds and strand of which are given by the large black arrows. (b) Log-log RPKM plots comparing merged PRO-seq and RNAseq libraries for control and heat-shock conditions. Genes are colored by RNA type. Spearman’s rank correlation coefficients (ρ) and Pearson’s correlation coefficients (r) are inset. (c) Box plots show the RPKM distribution for small non-coding RNAs and tRNAs across control and heat-shock conditions; 1 was added to all counts before normalization to facilitate plotting on a log scale. Black lines represent medians. P-values from two-sided Wilcoxon signed-rank tests are reported for each RNA type + treatment pair.
