Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| E. coli BW25113 | CGSC | Cat# 7636 |
| E. coli ATCC 25922 | ATCC | Cat# 25922 |
| E. coli K-12 MG1655 | ATCC | Cat# 700926 |
| E. coli W3110 | CGSC | Cat# 4474 |
| P. aeruginosa PAO1 | ATCC | Cat# 47085 |
| K. pneumoniae ATCC 13883 | ATCC | Cat# 13883 |
| A. baumannii ATCC 17978 | ATCC | Cat# 17978 |
| Chemicals, peptides, and recombinant proteins | ||
| Semapimod hydrochloride | BOC Sciences | Cat# B2693–462782 |
| Drug Repurposing Hub | Broad Institute | https://repo-hub.broadinstitute.org/repurposing |
| Broad Institute 800K Compound Database | Broad Institute | https://github.com/jackievaleri/nontoxic_stat_phase_killing_abx |
| 1-N-phenylnaphthylamine (NPN) | Sigma-Aldrich | Cat# 104043 |
| E. coli LPS | Sigma-Aldrich | Cat# L3129 |
| K. pneumoniae LPS | Sigma-Aldrich | Cat# L4268 |
| P. aeruginosa LPS | Sigma-Aldrich | Cat# L9143 |
| BODIPY-cadaverine | Molecular Probes | Cat# D6251 |
| LAL reagent | Thermo Scientific | Cat# 88282 |
| 250 U/μl benzonase | Sigma-Aldrich | Cat# E1014–25KU |
| 100× Halt Protease Inhibitor Cocktail | Life Technologies | Cat# 87786 |
| IGEPAL® CA-630 viscous liquid (NP-40) | Sigma-Aldrich | Cat# I3021–50ML |
| DC Protein Assay | Bio-Rad | Cat# 5000116 |
| Tris(2-carboxyethyl)phosphine (TCEP) | Pierce | Cat# 20490 |
| Methyl methanethiosulfonate (MMTS) | Thermo Fisher Scientific | Cat# 23011 |
| Ethyl alcohol, Pure 200 proof, HPLC grade | Sigma-Aldrich | Cat# 459828–1L |
| Triethylammonium bicarbonate buffer 1M (TEAB) | Sigma-Aldrich | Cat# T7408–100ML |
| Pierce Quantitative Fluorometric Peptide Assay | Thermo Fisher Scientific | Cat# 23290 |
| TMT10plex Isobaric Label Reagent Set | Thermo Fisher Scientific | Cat# 90110 |
| 50% hydroxylamine | Thermo Fisher Scientific | Cat# 90115 |
| Pierce high pH fractionation kit | Thermo Fisher Scientific | Cat# 84868 |
| Ultra-high-performance liquid chromatography (UPLC)-MS acetonitrile | Thermo Fisher Scientific | Cat# A9561 |
| Deposited data | ||
| DNA sequencing of semapimod evolution | This study – deposited in SRA | PRJNA1010194 |
| Thermal proteome profiling | This study – deposited in PRIDE | https://doi.org/10.6019/PXD044230 |
| Raw and analyzed data | This paper | https://github.com/jackievaleri/nontoxic_stat_phase_killing_abx |
| Experimental models: Cell lines | ||
| HepG2 | ATCC | Cat# HB-8065 |
| HEK-293 | ATCC | Cat# CRL-1573 |
| Rat Sprague Dawley Red Blood Cells | Innovative Research | Cat# IRTSDRBC |
| Recombinant DNA | ||
| pGDP2-mcr-1 plasmid | Addgene | pGDP2 MCR-1 was a gift from Gerard Wright (Addgene plasmid #118404) |
| Software and algorithms | ||
| Prism 9 | Graphpad | www.graphpad.com/scientific-software/prism/ |
| Original code | This paper |
https://github.com/jackievaleri/nontoxic_stat_phase_killing_abx and DOI: 10.5281/zenodo.8401264 |
| Chemprop | Yang et al., 2019 | https://github.com/chemprop/chemprop |
| RDKit | Landrum, 2010 | https://www.rdkit.org |
| Plotly Express | Sievert, 2020 | https://plotly-r.com |
| Scikit-Learn | Pedregosa et al., 2011 | https://scikit-learn.org/stable/ |
| Bcl-convert | Illumina | support.illumina.com/sequencing/sequencing_software/bcl-convert.html |
| Burrows-Wheeler transform | Li and Durbin, 2009 | github.com/lh3/bwa |
| Pilon | Walker et al., 2014 | https://software.broadinstitute.org/software/pilon/ |
| HISAT2 | Kim et al., 2019 | http://daehwankimlab.github.io/hisat2/ |
| featureCounts | Liao et al., 2014 | https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts |
| edgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| MicrobeJ | Ducret et al., 2016 | https://www.microbej.com/download-2/ |
| Fiji | Schindelin et al., 2012 | https://imagej.net/software/fiji/ |
| TPP | Franken et al., 2015 | https://www.bioconductor.org/packages/release/bioc/html/TPP.html |