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. 2022 Jun 9;25(7):104562. doi: 10.1016/j.isci.2022.104562
REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains

Escherichia coli EcNR2 Addgene Addgene #26931

Chemicals, peptides, and recombinant proteins

LB growth medium AmericanBio N/A
Solid chemicals: amino acids (phenylalanine, tryptophan, tyrosine), antibiotics (carbenicillin, spectinomycin), inducers (anhydrotetracycline, vanillic acid), trace minerals (Table S2), vitamins (Table S2) SigmaAldrich N/A
Colicin E1 for tolC counterselections This paper N/A

Experimental models: Organisms/strains

E. coli EcNR2.ΔpheA, ΔtrpDE, ΔtyrA, ΔpheA.ΔtrpDE, ΔtrpDE.ΔtyrA, ΔtyrA.ΔpheA, ΔpheA.ΔtrpDE.ΔtyrA, ΔpheA.ΔtrpDE.ΔtyrA.entA This paper CFH748-755

Oligonucleotides

MAGE oligo for aroF-FIM:
T∗T∗CAGTTGTTCCGGAGTCATTAAAACCTGTTCGTCG
GTAATATGTACTTTATTCAGCGCGTCTTTTTGcatGATG
GCGATCCTGTTTAT
This paper oCFH007
MAGE oligo for aroG-FIM:
T∗G∗CGCCCCAGCTCATCAGGTCAGCGAGATATTGT
GGGGTGATCATGTTGAGAAACTCACCTGCCGCTGG
CAGACCGCTGTCGTTAATATC
This paper oCFH008
Primers for cloning pPAF-v5 and pGFP-RFP This paper rCFH404-415
MAGE oligos for knockout of tolC insertions at pheA, trpDE, tyrA, and entA This paper oCFH026-29
Primers for amplifying tolC cassettes to recombiner into pheA, trpDE, tyrA, entA, and tyrR This paper rCFH334-337, 344-347, 511-512

Recombinant DNA

pPAF-v5 This paper CFH489
pGFP-RFP This paper CFH496
papBAC synthetic genes GenScript N/A

Software and algorithms

Python scripts for OptForce simulations This paper https://doi.org/10.5281/zenodo.6569900
Python v2.7.11 for Unix Python Software Foundation www.python.org
MATLAB r2019a for doubling time calculations MathWorks Inc https://www.mathworks.com
Gurobi Optimizer v9.0.0 Gurobi Optimization https://www.gurobi.com
COBRApy Toolbox v0.9.1 cobrapy - constraint-based metabolic modeling in Python https://opencobra.github.io/cobrapy/

Other

SCC Shared Computing Cluster, SCC1, 2 fourteen-core 2.4 GHz Intel Xeon E5-2680v4, 256 Gb RAM, 2 nodes Boston University Research Computing, Massachusetts Green High Performance Computing Center (MGHPCC), Holyoke, MA https://www.bu.edu/tech/support/research/computing-resources/scc/
Yale West Campus Analytical Core Yale University https://wcac.yale.edu
Experimental data and MATLAB analysis code for Figure 1, Figure 3 and 3 This paper https://doi.org/10.5281/zenodo.6569900