Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Eschericia coli) | Dh5a | |||
| Strain, strain background (M. smegmatis) |
ParB-mCherry | Santi and McKinney, 2015 | ||
| Strain, strain background (M. smegmatis) | See Supplementary file 1 | |||
| Recombinant DNA reagent | plJR962 | Rock et al., 2017 | ||
| Recombinant DNA reagent | See Supplementary file 1 | |||
| Sequence-based reagent | See Supplementary file 1 | |||
| Commercial assay or kit | OneTaq Master Mix | NEB | NEB M0482L | |
| Commercial assay or kit | Esp31-FastDigest | Thermo | FD0454 | |
| Commercial assay or kit | Zyppy-96 Plasmid Miniprep Kit | Zymo | D4041 | |
| Commercial assay or kit | FastRNA Blue Kit | MP Biomedicals | MP6025050 | |
| Commercial assay or kit | DNAse | NEB | NEB M0303S | |
| Commercial assay or kit | Poly(A) Polymerase | NEB | NEB M0276L | |
| Commercial assay or kit | Zymo RNA Clean and Concentrator-5 | Zymo | R1 013 | |
| Commercial assay or kit | Ribo-Zero rRNA Removal Kit | Illumina | MRZMB126 | |
| Commercial assay or kit | Nanopore Direct RNA Sequencing Kit | Oxford Nanopore Technologies | SQK-RNA002 | |
| Commercial assay or kit | Nanopore Direct cDNA Sequencing Kit | Oxford Nanopore Technologies | SQK-DCS109 | |
| Commercial assay or kit | NEBNext Q5 High-Fidelity Polymerase Master Mix | NEB | NEB M0543L | |
| Commercial assay or kit | QIAquick PCR purification kit | Qiagen | 28106 | |
| Commercial assay or kit | T4 Ligase | NEB | NEB M0202M | |
| Commercial assay or kit | SapI | NEB | NEB R0569S | |
| Chemical compound, drug | See Supplementary file 1 | |||
| Software algorithm | FIJI | Schindelin et al., 2012 | ||
| Software algorithm | MicrobeJ | Ducret et al., 2016 | ||
| Software algorithm | R | |||
| Software algorithm | UMAP | Lel et al., 2018 | ||
| Software algorithm | hdbscan | Lel et al., 2017 | ||
| Software algorithm | tSNE | Maaten and Hinton, 2008 | ||
| Software algorithm | Minimap2 | Li, 2018 | ||
| Software algorithm | samtools | Li et al., 2009 | ||
| Software algorithm | deepTools2 | Ramírez et al., 2016 | ||
| Software algorithm | featureCounts | Liao et al., 2014 | ||
| Software algorithm | DESeq2 | Love et al., 2014 | ||
| Software algorithm | Iris | Kritikos et al., 2017 |