Appendix 5—key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Escherichia coli) | E. coli K12 | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔYieP | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔGlpR | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔArcA | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔLrhA | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔPhoP | E. coli Stock Center | ||
| Cell line (Escherichia coli) | E. coli ΔHdfR | E. coli Stock Center | ||
| Strain, strain background (Escherichia coli) |
E. coli ΔGlpR in K12 strain |
This paper | Knockout transferred to E. coli K12 | |
| Strain, strain background (Escherichia coli) |
E. coli ΔArcA in K12 strain |
This paper | Knockout transferred to E. coli K12 | |
| Strain, strain background (Escherichia coli) |
E. coli ΔLrhA in K12 strain |
This paper | Knockout transferred to E. coli K12 | |
| Strain, strain background (Escherichia coli) |
E. coli ΔPhoP in K12 strain |
This paper | Knockout transferred to E. coli K12 | |
| Strain, strain background (Escherichia coli) |
E. coli ΔHdfR in K12 strain |
This paper | Knockout transferred to E. coli K12 | |
| Chemical compound, drug | Q5 Polymerase | Qiagen | Cat. : M0491L | |
| Chemical compound, drug | qPCR master mix | QuantaBio | Cat. : 101414–166 | |
| Chemical compound, drug | Lysyl Endopeptidase | Wako Chemicals | Cat. : 125–05061 | |
| Commercial assay or kit | RNEasy Mini kit | Qiagen | Cat. : 74104 | |
| Chemical compound, drug | RNAprotect bacteria reagent |
Qiagen | Cat. : 76506 | |
| Software, algorithm | mpathic | Kinney Lab Ireland and Kinney, 2016 | ||
| Software, algorithm | FastX | Hannon Lab | RRID:SCR_005534 | |
| Software, algorithm | FLASH | CBCB | RRID:SCR_005531 | |
| Other | Oligo Pool | Twist Bioscience | ||
| Sequence-based reagent | fwd oligo 101 | IDT | TTCGTCTTCACCT CGAGCACGCTTATT CGTGCCGTGTTAT | |
| Sequence-based reagent | fwd oligo 102 | IDT | TTCGTCTTCACCTC GAGCACTTTGCTT CAGTCAGATTCGC | |
| Sequence-based reagent | fwd oligo 103 | IDT | TTCGTCTTCACCT CGAGCACGTCGAGT CCTATGTAACCGT | |
| Sequence-based reagent | fwd oligo 104 | IDT | TTCGTCTTCACCT CGAGCACGTAAGAT GGAAGCCGGGATA | |
| Sequence-based reagent | fwd oligo 105 | IDT | TTCGTCTTCACCT CGAGCACGGTGTCGC AACATGATCTAC | |
| Sequence-based reagent | fwd oligo 106 | IDT | TTCGTCTTCACCT CGAGCACGTGCTAAG TCACACTGTTGG | |
| Sequence-based reagent | fwd oligo 107 | IDT | TTCGTCTTCACCT CGAGCACTCTAAACA GTTAGGCCCAGG | |
| Sequence-based reagent | fwd oligo 108 | IDT | TTCGTCTTCACCT CGAGCACGTCTTTAT ACTTGCCTGCCG | |
| Sequence-based reagent | fwd oligo 109 | IDT | TTCGTCTTCACCT CGAGCACCACCGCGA TCAATACAACTT | |
| Sequence-based reagent | fwd oligo 110 | IDT | TTCGTCTTCACCT CGAGCACTTCGGATA GACTCAGGAAGC | |
| Sequence-based reagent | fwd oligo 111 | IDT | TTCGTCTTCACCT CGAGCACCCATTGAT AGATTCGCTCGC | |
| Sequence-based reagent | fwd oligo 112 | IDT | TTCGTCTTCACCT CGAGCACTTTTCTAC TTTCCGGCTTGC | |
| Sequence-based reagent | fwd oligo 113 | IDT | TTCGTCTTCACCT CGAGCACATGACTAT TGGGGTCGTACC | |
| Sequence-based reagent | fwd oligo 114 | IDT | TTCGTCTTCACCT CGAGCACTCGACAAT AGTTGAGCCCTT | |
| Sequence-based reagent | fwd oligo 115 | IDT | TTCGTCTTCACCT CGAGCACGAGCCATG TGAAATGTGTGT | |
| Sequence-based reagent | fwd oligo 116 | IDT | TTCGTCTTCACCT CGAGCACCGTATACG TAAGGGTTCCGA | |
| Sequence-based reagent | fwd oligo 117 | IDT | TTCGTCTTCACCT CGAGCACTTATGATG TCCGGATACCCG | |
| Sequence-based reagent | fwd oligo 118 | IDT | TTCGTCTTCACCT CGAGCACTCTTAGAA ATCCACGGGTCC | |
| Sequence-based reagent | rev oligo 101 | IDT | TGTAAAACGACGG CCAGTGACTAGCGC TGAGGAGAAGCCT AATAGGGCACAGC AATCAAAAGTA | |
| Sequence-based reagent | rev oligo 102 | IDT | TGTAAAACGACG GCCAGTGAGGAGCGC TGAGGAGAAGCC TAATACCGGGATT CAGTGATTGAAC | |
| Sequence-based reagent | rev oligo 103 | IDT | TGTAAAACGACG GCCAGTGAGTCCC GCTGAGGAGAAG CCTAATATGAAGAT ATGACGACCCCTG | |
| Sequence-based reagent | rev oligo 104 | IDT | TGTAAAACGACGG CCAGTGACCGACGCT GAGGAGAAGCCTAA TATTCCACAGCTC TATGAGGTG | |
| Sequence-based reagent | rev oligo 105 | IDT | TGTAAAACGACGG CCAGTGATTGGCGCT GAGGAGAAGCCTA ATAGCAAACATGA CTAGGAACCG | |
| Sequence-based reagent | rev oligo 106 | IDT | TGTAAAACGACGG CCAGTGAGATACGC TGAGGAGAAGCC TAATACCGGGACG AGATTAGTACAA | |
| Sequence-based reagent | rev oligo 107 | IDT | TGTAAAACGACGGC CAGTGAACTCCGCT GAGGAGAAGCCTA ATACACGCCAGTT GTGAACATAA | |
| Sequence-based reagent | rev oligo 108 | IDT | TGTAAAACGACG GCCAGTGATACTCGC TGAGGAGAAGC CTAATACAAAGGC CAAATCAGTTCCA | |
| Sequence-based reagent | rev oligo 109 | IDT | TGTAAAACGACGGC CAGTGACCAACGCT GAGGAGAAGCCT AATAGGTGCATGGG AGGAACTATA | |
| Sequence-based reagent | rev oligo 110 | IDT | TGTAAAACGACG GCCAGTGAAGGCCGC TGAGGAGAAGCCT AATATGCATGGGT CTGTCTATTGT | |
| Sequence-based reagent | rev oligo 111 | IDT | TGTAAAACGACGGC CAGTGAAATTCGC TGAGGAGAAGCCT AATACTCCTATGCT AGCTCGACTC | |
| Sequence-based reagent | rev oligo 112 | IDT | TGTAAAACGACG GCCAGTGATTGT CGCTGAGGAGAAG CCTAATAATGGTA AGAAGCTCCCACAA | |
| Sequence-based reagent | rev oligo 113 | IDT | TGTAAAACGACGGC CAGTGATTTACGCT GAGGAGAAGCCTA ATACTATGGTCA TTCCCGTACGA | |
| Sequence-based reagent | rev oligo 114 | IDT | TGTAAAACGACGGC CAGTGAACCGCGCT GAGGAGAAGCCTA ATATAATCGGCT ACGTTGTGTCT | |
| Sequence-based reagent | rev oligo 115 | IDT | TGTAAAACGACGGC CAGTGATGGCCGC TGAGGAGAAGC CTAATATGACTCGA TCCTTTAGTCCG | |
| Sequence-based reagent | rev oligo 116 | IDT | TGTAAAACGACGG CCAGTGAGGCCCGC TGAGGAGAAGC CTAATAACGCTTT GTGTTATCCGATG | |
| Sequence-based reagent | rev oligo 117 | IDT | TGTAAAACGACGG CCAGTGAGGTGCG CTGAGGAGAAG CCTAATAACCACG GTGGAGTATACATC | |
| Sequence-based reagent | rev oligo 118 | IDT | TGTAAAACGACG GCCAGTGACAATCG CTGAGGAGAAGC CTAATAGGCACCA GGTACATATCTCA | |
| Sequence-based reagent | mRNA rev | IDT | GCAGGGGATAA TATTGCCCA | |
| Sequence-based reagent | fwd sequencing 94 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTGACC TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 95 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTCAGT TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 96 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTTCTA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 97 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTAGAG TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 98 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTGCAT TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 99 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTCTTA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 100 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTTAGC TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 101 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTCAAG TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 102 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTGTAC TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 103 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTTGAA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 104 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTTCGT TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 105 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTATGC TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 106 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTGTCA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 107 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTCTCA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | fwd sequencing 108 | IDT | AATGATACGGCGACCAC CGAGATCT ACACTCTT TCCCTACACGACGC TCTTCCGATCTAGTA TATTAGGCTT CTCCTCAGCG | |
| Sequence-based reagent | rev sequencing | IDT | AAGCAGAAGACGGCAT ACGAGATCGGT CTCG GCATTCCTGCTGAACC GCTCTTCCGATCTCAAA GCAGGGGATAA TATTGCCCA | |
| Other | Streptavin coated dynabeads | Thermo Fisher | Cat. : 65601 | |
| Database | RegulonDB | RRID:SCR_003499 | ||
| Database | EcoCyc | RRID:SCR_002433 |