Fig. 2

Identification and confirmation of small asRNAs. a Genes with asRNAs encoded opposite to them are functionally categorized using the following abbreviations: CD, cell division; CE, cell envelope; CM, cell motility; MT, metabolism; PD, protein degradation and folding; SR, stress response; TL, translation; TP, transporter; TR, transcription; RM; RNA metabolism; DM, DNA metabolism; VM, vitamin metabolism and U, unknown. asRNAs (SR0493 and SR0104) identified by sRNA-seq were confirmed via Northern blot analyses for as-bb0155 and as-bb0612. b and d The deep sequencing results are displayed in a coverage map of an overlay of the two rep0 libraries sequenced deeply for sRNA peak calling (Peak) and the overlay of the two biological replicates rep1, rep2 at both 23 °C and 37 °C. The height at each position indicates the normalized number of reads that mapped to that base. The – strand coverage is shown in blue. Note that the y-axis scale is different between the peak calling libraries (peak) and the biological replicates used for differential expression analyses (indicated by the grey numbers in brackets). The genomic context is illustrated below the coverage maps: black arrows indicate the annotated ORFs, the yellow box indicates the region called as a small asRNA by our peak finder and the wavy line is the putative transcript determined by Northern blot. The red line represents the location of the oligonucleotide probes used for the Northern blot. c and e Northern blot analyses of total RNA fractionated on a denaturing polyacrylamide gel, blotted to a nylon membrane, and hybridized with oligonucleotides. The predicted transcripts are denoted and marked with the appropriate band (^ for sRNA) in the Northern blot. Two independent experiments were performed and representative data are shown