Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | |||
| Terminal Transferase (TdT) | New England Biolabs | M0315S | |
| HinP1 | New England Biolabs | R0124S | |
| AlwNI | New England Biolabs | R0514S | |
| BglII | New England Biolabs | R0144S | |
| T4 DNA ligase | New England Biolabs | M0202S | |
| Phusion Polymerase | New England Biolabs | M0530S | |
| 2’-deoxy-cytidine-5´-triphosphate (dCTP) | New England Biolabs | N0446S | |
| 2’,3’-dideoxy-cytidine-5’-triphosphate (ddCTP) | Thermo Scientific | 45–001-339 | |
| 4′,6-Diamidine-2′-phenylindole dihydrochloride (DAPI) | Sigma Aldrich | 10236276001 | |
| FM 4–64 Dye | Invitrogen | T13320 | |
| Critical Commercial Assays | |||
| Wizard Genomic DNA Purification Kit | Promega | A1120 | |
| Quick Ligation Kit | New England Biolabs | M2200L | |
| Qiaquick PCR Cleanup Kit | Qiagen | 28106 | |
| Axygen™ AxyPrep Mag™ PCR Cleanup Kits | Thermo Scientific | 14–223-227 | |
| Deposited Data | |||
| Genemoic Sequencing Data | This Study | https://www.ncbi.nlm.nih.gov/sra/PRJNA597349 | |
| Experimental Models: Organisms/Strains | |||
| E. coli : CW45 : MP1999 with cat at nt 35040 of Mu | (Choi et al. 2010) | CW45 | |
| E. coli : DMW11 : MG1655 with Mu:cat at nt 4203381 (Bin 91) | This study | DMW11 | |
| E. coli : DMW14 : MG1655 with Mu:cat at nt 3425548 (Bin 83) | This study | DMW14 | |
| E. coli : DMW15 : MG1655 with Mu:cat at nt 263131 (Bin 5) | This study | DMW15 | |
| E. coli : DMW16 : MG1655 with Mu:cat at nt 517329 (Bin 11) | This study | DMW16 | |
| E. coli : DMW18 : MG1655 with Mu:cat at nt 3547885 (Bin 76) | This study | DMW18 | |
| E. coli : DMW19 : MG1655 with Mu:cat at nt 1947582 (Bin 41) | This study | DMW19 | |
| E. coli : DMW21 : MG1655 with Mu:cat at nt 50316 (Bin 1) | This study | DMW21 | |
| E. coli : DMW22 : MG1655 with Mu:cat at nt 3339450 (Bin 72) | This study | DMW22 | |
| E. coli : DMW24 : MG1655 with Mu:cat at nt 2555144 (Bin 55) | This study | DMW24 | |
| E. coli : DMW25 : MG1655 with Mu:cat at nt 1247622 (Bin 25) | This study | DMW25 | |
| E. coli : DMW26 : MG1655 with Mu:cat at nt 1733701 (Bin 37) | This study | DMW26 | |
| E. coli : DMW27 : MG1655 with Mu:cat at nt 398930 (Bin 8) | This study | DMW27 | |
| E. coli : DMW30 : MG1655 with Mu:cat at nt 1235556 (Bin 26) | This study | DMW30 | |
| E. coli : DMW32 : MG1655 with Mu:cat at nt 2856391 (Bin 61) | This study | DMW32 | |
| E. coli : DMW33 : MG1655 with Mu:cat at nt 792226 (Bin 17) | This study | DMW33 | |
| E. coli : DMW34 : MG1655 with Mu:cat at nt 225365 (Bin 4) | This study | DMW34 | |
| E. coli : DMW37 : MG1655 with Mu:cat at nt 2738859 (Bin 59) | This study | DMW37 | |
| E. coli : DMW38 : MG1655 with Mu:cat at nt 4554492 (Bin 98) | This study | DMW38 | |
| E. coli : DMW41 : MG1655 with Mu:cat at nt 2937424 (Bin 63) | This study | DMW41 | |
| E. coli : DMW42 : MG1655 with Mu:cat at nt 4209762 (Bin 90) | This study | DMW42 | |
| E. coli : DMW44 : MG1655 with Mu:cat at nt 3447802 (Bin 74) | This study | DMW44 | |
| E. coli : DMW47 : MG1655 with Mu:cat at nt 2219564 (Bin 47) | This study | DMW47 | |
| E. coli : DMW48 : MG1655 with Mu:cat at nt 2440295 (Bin 52) | This study | DMW48 | |
| E. coli : DMW51 : MG1655 with Mu:cat at nt 2286196 (Bin 49) | This study | DMW51 | |
| E. coli : DMW54 : MG1655 with Mu:cat at nt 4053514 (Bin 87) | This study | DMW54 | |
| E. coli : DMW57 : MG1655 with Mu:cat at nt 1657887 (Bin 35) | This study | DMW57 | |
| E. coli : DMW58 : MG1655 with Mu:cat at nt 3700134 (Bin 79) | This study | DMW58 | |
| E. coli : DMW59 : MG1655 with Mu:cat at nt 4385978 (Bin 94) | This study | DMW59 | |
| E. coli : DMW61:MG 1655 with Mu:cat at nt 995741 (Bin 21) | This study | DMW61 | |
| E. coli : DMW63 : MG1655 with Mu:cat at nt 3119489 (Bin 67) | This study | DMW63 | |
| E. coli : DMW64 : MG1655 with Mu:cat at nt 1590702 (Bin 34) | This study | DMW64 | |
| E. coli : DMW66 : MG1655 with Mu:cat at nt 3045056 (Bin 65) | This study | DMW66 | |
| E. coli : DMW69 : MG1655 with Mu:cat at nt 1799218 (Bin 38) | This study | DMW69 | |
| E. coli : DMW71 : MG1655 with Mu:cat at nt 1465154 (Bin 31) | This study | DMW71 | |
| E. coli : DMW72 : MG1655 with Mu:cat at nt 1939066 (Bin 42) | This study | DMW72 | |
| E. coli : DMW104 : MG1655, aidB:parSP1-cat | (Nielsen et al., 2006) | DMW104 | |
| E. coli : DMW106 : MG1655, araC:parST1-kan | (Nielsen et al., 2006) | DMW106 | |
| E. coli : DMW110 : MG1655, ycdN:parST1-cat | (Nielsen et al., 2006) | DMW110 | |
| E. coli : DMW112 : MG1655, feaR:parSP1-kan | (Nielsen et al., 2006) | DMW112 | |
| E. coli : DMW134 : MG1655, ycdN:parST1-cat, yfgE:parSP1-kan | (Nielsen et al., 2006) | DMW134 | |
| E. coli : DMW138 : MG1655, ycdN:parST1-cat, yfgE:parSP1-kan, Mu:cat at nt 3867127 (Bin 83) | This study, DMW134 | DMW138 | |
| E. coli : DMW150 : MG1655 dnaQ:parSP1-kan | This study | DMW150 | |
| E. coli : DMW151 : MG1655 dnaQ:parSP1-kan, dnaB:parST1 | This study, DMW150 | DMW151 | |
| E. coli : DMW152 : MG1655 yibT:;parSP1-kan | This study | DMW152 | |
| E. coli : DMW153 : MG1655 yibT:parSP1, ytfP:parST1 | This study, DMW151 | DMW153 | |
| E. coli : DMW155 : MG1655 dnaQ:parSP1-kan, dnaA:parST1 | This study, DMW150 | DMW155 | |
| E. coli : DMW156 : MG1655 dnaA:parST1-cat | This study | DMW156 | |
| E. coli : DMW157 : MG1655 dnaA:parST1-cat, ygbI:parSP1-kan | This study, DMW156 | DMW157 | |
| E. coli : DMW159 : MG1655 aroG:parST1-cat | This study | DMW159 | |
| E. coli : DMW160 : MG1655 aroG:parST1-cat, pheL:parSP1-kan | This study, DMW156 | DMW160 | |
| E. coli : DMW191 : DMW22 ΔIhf:kan | This study | DMW191 | |
| E. coli : DMW192 : DMW22 Δfis:kan | This study | DMW192 | |
| E. coli : DMW193 : DMW22 ΔhuB:kan | This study | DMW193 | |
| E. coli : DMW194 : DMW22 ΔmatP:kan | This study | DMW194 | |
| E. coli : DMW200 : DMW22 ΔhupA:kan | This study | DMW200 | |
| E. coli : DMW201 : DMW22 ΔhupA/B:kan | This study | DMW201 | |
| E. coli : DMW204 : DMW22 ΔmukB:kan | This study | DMW204 | |
| E. coli : DMW205 : DMW15 ΔmukB:kan | This study | DMW205 | |
| E. coli : DMW206 : DMW33 ΔmukB:kan | This study | DMW206 | |
| E. coli : DMW207 : DMW57 ΔmukB:kan | This study | DMW207 | |
| E. coli : DMW208 : DMW37 ΔmukB:kan | This study | DMW208 | |
| E. coli : DMW209 : DMW11 ΔmukB:kan | This study | DMW209 | |
| E. coli : DMW220 : MG1655 rrnD:parSP1-kan, rrnG:parST1 | (Gaal et al., 2016) | DMW220 | |
| E. coli : DMW221 : DMW24 Mu:cat Δnt 5138–7233 parSP1:kan at nt 5238 | This study | DMW221 | |
| E. coli : DMW235 : DMW69 ΔpheL:frt | This Study | DMW235 | |
| E. coli : DMW236 : DMW69 ΔpheL:frt, pheL:kan at nt 522930 | This Study | DMW236 | |
| E. coli : DMW237 : DMW69 ΔpheL:frt, pheL:kan at nt 1418108 | This Study | DMW236 | |
| Oligonucleotides | |||
| Please see Table S1 for oligonucleotide primers | This Study | N/A | |
| Plasmids | |||
| pFH2973 (CFP-Δ30ParBP1/ eGFP-Δ23ParBT1 expression vector, AmpR) | (Nielsen et al., 2006) | N/A | |
| pKD46 | (Datsenko and Wanner, 2000) | N/A | |
| pKD4 | (Datsenko and Wanner, 2000) | Addgene 45605 | |
| pDW33 (pKD4 pheL:kan, AmpR, KanR) | This study | N/A | |
| Software and Algorithms | |||
| MAPS (Python) | This Study | https://github.com/dmwalker/MuSeq | |
| Spot_detect.py (Python) | This Study | https://github.com/dmwalker/MuSeq | |
| LASSO Regression Analysis (R) | This Study | https://github.com/dmwalker/MuSeq | |
| Microscopy Analysis (Python) | This Study | https://github.com/dmwalker/MuSeq | |
| DL-POLY Classic | (Todorov et al., 2006) | https://www.ccp5.ac.uk/DL_POLY_CLASSIC | |
| Polymer simulation analysis (Python) | This study | https://github.com/dmwalker/MuSeq | |
| BWA-MEM | Li H., 2013 | https://sourceforge.net/projects/bio-bwa/ | |
| MATLAB | The Mathworks Inc | https://mathworks.com/products/matlab.html | |