REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Chemicals, Peptides, and Recombinant Proteins | ||
BamHI-HF | NEB | R3136S |
HindIII-HF | NEB | R3104S |
NotI-HF | NEB | R3189S |
BglII | NEB | R0144S |
NheI | NEB | R0131S |
XhoI | NEB | R0146S |
4-Nitroquinoline N-oxide | Sigma | N8141 |
Gibson Assembly Master Mix | NEB | E2611S |
Phusion High-Fidelity PCR Master Mix | Thermo | F531S |
Nano-Glo Luciferase Assay System | Promega | N1130 |
Critical Commercial Assays | ||
Nextera XT DNA Library Preparation Kit | Illumina | (FC-131-1024) |
GeneJET PCR Purification Kit | Thermo | K0701 |
GeneJET Genomic DNA purification Kit | Thermo | K0722 |
MasterPure complete DNA and RNA Purification Kit | Epicenter | MC85200 |
QIAquick PCR Purification Kit | QIAGEN | 28106 |
Deposited Data | ||
All fastq files and descriptions uploaded to Sequence Read Archive | NCBI SRA SUB4542953 |
Bioproject: PRJNA492467 |
Experimental Models: Cell Lines | ||
Human: Caco-2 epithelial cell line | ATCC | HTB-37; RRID:CVCL_0025 |
Harvested Bone Marrow Macrophages from BALB/c mice | N/A | Miller Lab |
Experimental Models: Organisms/Strains | ||
B. subtilis trpC2 pheA1 | Brehm et al., 1973 | HM1 |
B. subtilis trpC2 uvrA::mls | Bacillus stock center | HM713 |
B. subtilis trpC2 mfd::mls | Bacillus stock center | HM1720 |
S. typhimurium ST19 | Hayden et al., 2016 | HM1996 |
P. aeruginosa CF127 | Wolfgang et al., 2003 | HM2212 |
P. aeruginosa CF127 Δmfd | This study | HM2260 |
E. coli F’(kan) placOL2-62-lacZ | Dove et al., 1997 | HM2295 |
B. subtilis mfd::mls, trpC2 pheA1 | Million-Weaver et al., 2015 | HM2521 |
E. coli F’(kan) placOL2-62, pSIM27(tet) | This study | HM2602 |
B. subtilis uvrA::mls, trpC2 pheA1 | Million-Weaver et al., 2015 | HM2633 |
E. coli FW102 OL2-62-Nanoluc(hyg), pSIM27 | This study | HM2747 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19rpoB(19-142) | This study | HM2838 |
E. coli FW102 OL2-62-Nanoluc(hyg), pBRα, pACλCI Plac-CI-ST19mfd(1-450) | This study | HM2875 |
S. typhimurium ST19, pUC19 | This study | HM2880 |
S. typhimurium ST19 mfd::cat, pUC19 | This study | HM2881 |
S. typhimurium ST19 mfd::cat, pUC19-ST19mfd | This study | HM2882 |
S. typhimurium ST19 mfd::cat, pUC19-ST19mfdL499R | This study | HM2886 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19mfd(1-450), pBRα Plac-a-ST19UvrA(88-505) | This study | HM2913 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα Plac-a-ST19mfd (RID) | This study | HM2920 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα Plac-a-ST19mfd (RID) L499R | This study | HM2921 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα | This study | HM2925 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19mfd (RID) | This study | HM2926 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19UvrA(88-505) | This study | HM2949 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19mfdR165A, pBRα Plac-a-ST19UvrA(88-505) | This study | HM2962 |
S. typhimurium ST19 mfd::cat, pUC19-Mtbmfd | This study | HM3134 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-Mtbmfd(334-651), pBRα | This study | HM3193 |
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-Mtbmfd(334-651), pBRα Plac-a-ST19rpoB(19-142) | This study | HM3225 |
S. typhimurium ST19 uvrA::kan | This study | HM3245 |
S. typhimurium ST19 ST19mfd::Mtbmfd-kan | This study | HM3406 |
S. typhimurium ST19 mfd::cat | This study | HM3429 |
S. typhimurium ST19, pMMB67EH | This study | HM3585 |
S. typhimurium ST19 mfd::cat, pMMB67EH | This study | HM3586 |
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfd | This study | HM3590 |
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfdR165A | This study | HM3666 |
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfdL499R | This study | HM3667 |
M. tuberculosis H37Rv | ATCC | ATCC 27294 |
M. tuberculosis H37Rv mfd::hyg | This study | MR02 |
Oligonucleotides | ||
Primer sequences provided in Table S3 | N/A | N/A |
Recombinant DNA | ||
pHM443 | This study | pHM443 |
pHM453 | This study | pHM453 |
pHM457 | This study | pHM457 |
pHM458 | This study | pHM458 |
pHM474 | This study | pHM474 |
pHM480 | This study | pHM480 |
pHM481 | This study | pHM481 |
pHM484 | This study | pHM484 |
pHM494 | This study | pHM494 |
pHM499 | This study | pHM499 |
pHM550 | This study | pHM550 |
pHM566 | This study | pHM566 |
pHM629 | This study | pHM629 |
pHM649 | This study | pHM649 |
pHM650 | This study | pHM650 |
pHM651 | This study | pHM651 |
pHM661 | This study | pHM661 |
pHM662 | This study | pHM662 |
pBRα | Addgene | Addgene 53731 |
pBRα-β-flap | Addgene | Addgene 53734 |
pACλCI | Addgene | Addgene 53730 |
pACλCI-β-flap | Addgene | Addgene 53733 |
pEX18 | Gift from Dr. Matthew Parsek | pEX18 |
pKD3 | Addgene | Addgene 45604 |
pKD13 | Miller Lab Stock | pKD13 |
pKD46 | Miller Lab Stock | pKD46 |
pMMBEH67 | Miller Lab Stock | pMMBEH67 |
pNIT | Sherman Lab Stock | pNIT |
pNL1.1 | Promega | Promega N1441 |
pSIM27 | Gift from Dr. Don Court | pSIM27 |
pUC19 | Addgene | Addgene 50005 |
Software and Algorithms | ||
SAMtools | Li et al., 2009 | N/A |
Bowtie 2 | Langmead and Salzberg, 2012 | N/A |
breseq | Deatherage and Barrick, 2014 | N/A |
Prism 7 Graphpad | N/A | N/A |