KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| M. smegmatis: Strain mc2155 | ATCC | ATCC 700084 |
| pHW64-pSmyc-SD1-mScarlet-RBS-mNeonGreen | This work | N/A |
| MSR-Dendra plasmid library | Addgene | https://www.addgene.org/Keith_Derbyshire/ |
| Chemicals, peptides, and recombinant proteins | ||
| Nile red | Sigma-Aldrich | Cat#N3013 |
| Hoechst 33342 | Thermo-Fisher | Cat#H3570 |
| Syto-17 | Thermo-Fisher | Cat#S7579 |
| FM 4-64 | Thermo-Fisher | Cat#T13320 |
| Chloramphenicol | Sigma-Aldrich | Cat#R4408 |
| Rifampicin | Sigma-Aldrich | Cat#R3501 |
| Bedaquiline | BioVision | Cat#9598 |
| Deposited data | ||
| Unprocessed imaging data of the MSR-Dendra library | Judd et al. 2021; This work | N/A |
| Unprocessed imaging data of reference strains | This work | N/A |
| GEMATRIA converted profiles | This work | https://github.com/jzrolling/MOMIA/blob/master/demo/MSR_dendra_GEMATRIA_compiled.npy |
| Time-lapse data of FtsZ-mCherry (CB954) | Wu et al., 2018 | N/A |
| Time-lapse data of other proteins specified in Figure 6E | This work | N/A |
| Experimental models: Organisms/strains | ||
| M. smegmatis: Strains of MSR-Dendra library | Judd et al. 2021; This work | https://msrdg.org/ |
| M. smegmatis: Strain HW188 (carrying pHW64) | This work | N/A |
| M. smegmatis: CB858 | Wu et al., 2018 | N/A |
| M. smegmatis: CB954 | Wu et al., 2018 | N/A |
| M. smegmatis: CB972 | Wu et al., 2018 | N/A |
| M. smegmatis: CB1163 | Wu et al., 2018 | N/A |
| M. smegmatis: CB991 | Wu et al., 2018 | N/A |
| M. smegmatis: CB989 | Wu et al., 2018 | N/A |
| M. smegmatis: CB913 | Wu et al., 2018 | N/A |
| Software and algorithms | ||
| Fiji | Schindelin et al., 2012 | https://fiji.sc/ |
| Python 3.7 | van Rossum and Drake, 2009 | https://www.python.org/downloads/release/python-370/ |
| Scikit-image v0.17.2 | Van Der Walt et al., 2014 | https://github.com/scikit-image/scikit-image/releases/tag/v0.17.2 |
| Numpy v1.19.4 | Harris et al., 2020 | https://github.com/numpy/numpy/releases/tag/v1.19.4 |
| Numba v0.51.2 | Lam et al., 2015 | https://github.com/numba/numba/releases/tag/0.51.2 |
| Scipy v1.5.4 | Virtanen et al., 2020 | https://github.com/scipy/scipy/tree/v1.5.4 |
| Scikit-learn v0.23.2 | Pedregosa et al., 2012 | https://github.com/scikit-learn/scikit-learn/releases/tag/0.23.2 |
| SAFEpy | Baryshnikova, 2016 | http://doi.org/10.1016/j.cels.2016.04.014 |
| Snfpy | Wang et al., 2014 | https://github.com/rmarkello/snfpy |
| UMAP | McInnes et al., 2018 | https://github.com/lmcinnes/umap |
| MOMIA v0.0.1 | This work | http://doi.org/10.5281/zenodo.5607009 |
| GEMATRIA v0.0.1 | This work | http://doi.org/10.5281/zenodo.5607009 |
| Other | ||
| Morphological profiles of M. smegmatis strains with CRISPRi mediated gene knockdown | de Wet et al., 2020 | https://osf.io/pdcw2/ |
| KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations of M. smegmatis CDSs. | Kanehisa, 2000 | https://www.genome.jp/entry/gn:T00434 |
| COG (Clusters of Orthologous Genes) annotations of M. smegmatis CDSs. | Galperin et al., 2021 | https://ftp.ncbi.nih.gov/pub/COG/COG2020/data/ |