KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and Virus Strains | ||
| Bacillus subtilis strains | This Paper | See Table S5 |
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Chemicals for MCCG Media | This Study | See Table S3 |
| Trichloroacetic Acid | Sigma | T6399 |
| Isopropanol | Macron | 3032–16 |
| 1M Tris pH 9.5 | Teknova | T1095 |
| Qubit BR RNA | ThermoFisher | Q10210 |
| Superase-IN RNase | ThermoFisher | AM2696 |
| PerfectHyb Plus Hybridization buffer | Sigma | H7033 |
| Glycoblue | ThermoFisher | AM9516 |
| Corning® 500 mL 0.2 μm Pore filter | Corning | 430773 |
| Select-a-size DNA Clean & Concentrator | Zymo | D4080 |
| NEBuilder HiFi DNA Assembly Master Mix | New England Biolabs | E2621S |
| DNase I recombinant, RNase-free (Roche) | Sigma-Aldrich | 4716728001 |
| Micrococcal nuclease | Roche | No longer available |
| T4 Polynucleotide Kinase (PNK) | New England Biolabs | M0201S |
| SuperScript III Reverse Transcriptase | ThermoFisher Scientific | 18080093 |
| CircLigase ssDNA ligase | Lucigen | CL4115K |
| Dynabeads MyOne Streptavidin C1 | ThermoFisher Scientific | 65001 |
| Q5 High-Fidelity DNA Polymerase | New England Biolabs | M0491L |
| T4 RNA ligase 2 truncated K277Q | J. Weissman | N/A |
| ATP, [γ-32P] | PerkinElmer | BLU502A250UC |
| SuperScript III Reverse Transcriptase | Thermo Fisher Scientific | 18080044 |
| G25 Sepharose columns | GE Healthcare Life Sciences | 27532501 |
| Critical Commercial Assays | ||
| RNeasy Mini kit | QIAGEN | 74104 |
| MICROBExpress Bacterial mRNA Enrichment Kit | ThermoFisher Scientific | AM190 |
| Oligo Clean & Concentrator | Zymo Research | D4060 |
| Deposited Data | ||
| Raw .fastq and processed .wig files from Ribosome profiling | This paper | GEO: GSE141389 |
| Northern blots raw data | This paper; Mendeley data | http://dx.doi.org/10.17632/f9kkszrtch.1 |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Bacillus subtilis strains | This Paper | See Table S5 |
| Oligonucleotides | ||
| Northern Blot assay probes | This paper | See Table S2 |
| RT-qPCR primers | This paper | See Table S2 |
| Library preparation primers | This paper | See Table S2 |
| Strain creation primers | This paper | See Table S2 |
| Competition experiment primers | This paper | See Table S2 |
| Recombinant DNA | ||
| Software and Algorithms | ||
| Bowtie v2.0.0b3 | Langmead et al. (2009) | http://bowtie-bio.sourceforge.net/index.shtml |
| Python 2.7 | Python Software Foundation | http://www.python.org |
| Other custom python scripts | This paper | Available upon request |
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| Other | ||
| Super Membrane Disc Filters, Pall Laboratory | VWR | 28147–980 |
| Grinding Jar Set, Stainless Steel | Qiagen | 69985 |
| TissueLyser II | Qiagen | 85300 |
| Novex TBE-Urea gels, 15% | ThermoFisher | EC6885BOX |
| Novex TBE-Urea gels, 10% | ThermoFisher | EC6875BOX |
| Novex TBE gels, 8% | ThermoFisher | EC62152BOX |