Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | MG1655 (WT) | this study | N/A | see Supplementary file 4 for derivatives |
| Antibody | mouse monoclonal anti-FLAG-M2-HRP | Sigma-Aldrich | Cat#A8592 | WB (1:2000) |
| Antibody | rabbit polyclonal anti-OmpC | Biorbyt | Cat#orb6940 | WB (1:500) |
| Antibody | donkey polyclonal peroxidase labeled anti-rabbit | GE Healthcare | Cat#NIF824 | WB (1:1000) |
| Recombinant DNA reagent | pBRplac | Guillier and Gottesman, 2006 | N/A | see Supplementary file 4 for derivatives |
| Recombinant DNA reagent | pNM46 (pBRplac-lacI) | this study | N/A | see Supplementary file 4 for derivatives |
| Recombinant DNA reagent | pKD46 | Datsenko and Wanner, 2000 | N/A | see Supplementary file 4 for derivatives |
| Recombinant DNA reagent | pMM1 | Stringer et al., 2014 | N/A | see Supplementary file 4 for derivatives |
| Sequence-based reagent | northern probes and primers | this study | N/A | see Supplementary file 4 |
| Chemical compound, drug | spermidine | Sigma-Aldrich | Cat#S2626-1G | |
| Other | TRIzol reagent | Thermo Fisher Scientific | Cat#15596018 | RNA extractions |
| Other | RNA-sequencing reagents | Melamed et al., 2018 | N/A | |
| Other | ureagel-8 | National Diagnostics | Cat#EC-838 | acrylamide northern solution |
| Other | ureagel complete | National Diagnostics | Cat#EC-841 | acrylamide northern solution |
| Other | NuSieve 3:1 agarose | Lonza | Cat#50090 | agarose for northern blotting |
| Other | 37% formaldehyde | Fisher Scientific | Cat#BP531-500 | |
| Other | RiboRuler high range RNA ladder | Thermo Fisher Scientific | Cat#SM1821 | |
| Other | RiboRuler low range RNA ladder | Thermo Fisher Scientific | Cat#SM1831 | |
| Other | Zeta-Probe blotting membrane | Bio-Rad | Cat#1620159 | northern membrane |
| Other | ULTRAhyb-oligo hybridization buffer | Thermo Fisher Scientific | Cat#AM8663 | |
| Other | γ-32P ATP | PerkinElmer | Cat#NEG035C010MC | |
| Other | T4 polynucleotide kinase | New England Biolabs | Cat#M0201L | |
| Other | Illustra MicroSpin G-50 columns | GE Healthcare | Cat#27533001 | |
| Other | mini-PROTEAN TGX gels | Bio-Rad | Cat#456–1086 | |
| Other | EZ-RUN pre-stained Rec protein ladder | Fisher Scientific | Cat#BP3603-500 | |
| Other | nitrocellulose membrane | Thermo Fisher Scientific | Cat#LC2000 | western membrane |
| Other | SuperSignal West Pico PLUS chemiluminescent substrate | Thermo Fisher Scientific | Cat#34580 | |
| Software, algorithm | lcdb-wf | ‘lcdb-wf’. Dale et al., GitHub Repository | v1.5.3 | https://github.com/lcdb/lcdb-wf |
| Software, algorithm | sra-tools | SRA Toolkit Development Team | v2.9.1_1 | http://ncbi.github.io/sra-tools/ |
| Software, algorithm | cutadapt | Martin, 2011 | v2.3 | https://github.com/marcelm/cutadapt |
| Software, algorithm | fastqc | Wingett and Andrews, 2018 | v0.11.8 | https://qubeshub.org/resources/fastqc |
| Software, algorithm | bwa | Li and Durbin, 2010 | v0.7.17 | http://bio-bwa.sourceforge.net/ |
| Software, algorithm | bowtie2 | Langmead and Salzberg, 2012 | v2.3.5 | http://bowtie-bio.sourceforge.net/bowtie2 |
| Software, algorithm | samtools | Li et al., 2009 | v1.9 | http://www.htslib.org/ |
| Software, algorithm | subread | Liao et al., 2013 | v1.6.4 | http://subread.sourceforge.net/ |
| Software, algorithm | multiqc | Ewels et al., 2016 | v1.7 | https://github.com/ewels/MultiQC |
| Software, algorithm | picard | ‘Picard Toolkit.’ 2019. Broad Institute, GitHub Repository | v2.20.0 | https://github.com/broadinstitute/picard |
| Software, algorithm | deeptools | Ramírez et al., 2016 | v3.2.1 | https://deeptools.readthedocs.io/ |
| Software, algorithm | termseq-peaks | ‘termseq-peaks.’ 2020. NICHD-BSPC, GitHub Repository | N/A | https://github.com/NICHD-BSPC/termseq-peaks |
| Software, algorithm | bedtools | Quinlan and Hall, 2010 | v2.27.1 | https://bedtools.readthedocs.io/ |
| Software, algorithm | pybedtools | Dale et al., 2011 | v0.8.0 | https://github.com/daler/pybedtools |
| Software, algorithm | ucsc-toolkit | Kent et al., 2010 | v357 | https://doi.org/10.1093/bioinformatics/btq351 |
| Software, algorithm | biopython SeqIO | Cock et al., 2009 | v1.73 | biopython.org |
| Software, algorithm | rhoterm-peaks | ‘rhoterm-peaks’ 2020. GitHub repository | N/A | https://github.com/gbaniulyte/rhoterm-peaks |
| Software, algorithm | CLG Genomics Workbench | Qiagen | v8.5.1 | alignment of DirectRNA-seq reads |
| Software, algorithm | CLUSTAL | Madeira et al., 2019 | v2.1 | https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| Software, algorithm | BOXSHADE | v3.21 | https://embnet.vital-it.ch/software/BOX_form.html | |
| Software, algorithm | Sfold | Ding et al., 2004 | v2.2 | http://sfold.wadsworth.org/cgi-bin/srna.pl |