KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and virus strains | ||
| E. coli barcoded deletion library | Laboratory of Hirotoda Mori | N/A |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| AMPure XP bead | Beckman Coulter | Cat#A63881 |
| KAPA HiFi HotStart ReadyMix | Kapa Biosystems | Cat#KK2602 |
| Difco M9 Minimal Media Salts, 5X | BD | Cat#248510 |
| Protein hydrolysate amicase | Sigma Aldrich | Cat#82514 |
| Tryptophan | Sigma Aldrich | Cat#T0254 |
| Uridine | Alfa Aesar | Cat#A15227-06 |
| Adenine sulfate | USBiological | Cat#A0865 |
| Biotin | Sigma Aldrich | Cat#B4639 |
| Niacin | Spectrum | Cat#NI100 |
| D-pantothenic acid | Sigma Aldrich | Cat#P5155 |
| Critical commercial assays | ||
| BioAnalyzer/Agilent High Sensitivity DNA Kit | Agilent | Cat# 5067-4626 |
| Qubit dsDNA high sensitivity assay | Thermo-fisher | Cat#Q32854 |
| Quick DNA Miniprep Plus Kit | Zymo | Cat#D4068 |
| Nextera XT Index Kit | Illumina | Cat#FC-131-1024 |
| MiniSeq High Output Reagent Kit, 75-cycles | Illumina | Cat#FC-420-1001 |
| MiniSeq High Output Reagent Kit, 150-cycles | Illumina | Cat#FC-420-1002 |
| MiSeq Reagent Kit v3, 150-cycles | Illumina | Cat#MS-102-3001 |
| Deposited data | ||
| Auxotroph screen | This study | PRJNA727839 |
| Assembly dynamics in nutrient-poor media | This study | PRJNA727852 |
| Assembly dynamics in nutrient-rich media | This study | PRJNA727847 |
| Pooled library in nutrient rich media | Rosener et al., 2020 | PRJNA645605 |
| Experimental models: cell lines | ||
| Experimental models: organisms/strains | ||
| Oligonucleotides | ||
| Forward primer for barcoded library: 5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-(4-6xN)-TGTAGGCTGGAGCTGCTTCG 3' | Rosener et al., 2020 | N/A |
| Reverse primer for barcoded library: 5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-GCAAATATTATACGCAAGGCGACAAG 3’ | Rosener et al., 2020 | N/A |
| Recombinant DNA | ||
| Software and algorithms | ||
| Cystoscape | Shannon et al., 2003 | https://cytoscape.org |
| Matlab(R2020a) | Mathworks | https://www.mathworks.com/downloads/ |
| Circa | OMGenomics | https://omgenomics.com/circa/ |
| DEBRA, R package | Akimov et al., 2020 | https://github.com/YevhenAkimov/DEBRA |
| GAGE, R package | Luo et al., 2009 | https://bioconductor.org/packages/release/bioc/html/gage.html |
| DESeq2, R package | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Code to analyze data and generate plot | This study | DOI: 10.5281/zenodo.5106763 |
| Other | ||