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. Author manuscript; available in PMC: 2023 Jul 25.
Published in final edited form as: Curr Biol. 2022 Jun 30;32(14):3059–3069.e7. doi: 10.1016/j.cub.2022.06.011

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial strains
Vibrio splendidus 76 12B01
Escherichia coli PIR1 Invitrogen, Waltham, MA, USA Cat#C101010
V. splendidus carrying a mKate-expressing, chloramphenicol resistant replicative plasmid pLL103 This paper 12B01 + pLL103
Escherichia coli PIR1 carrying pLL103 This paper PIR1 + pLL103
V. splendidus carrying an eGFP-expressing, chloramphenicol resistant replicative plasmid pLL104 This paper 12B01 + pLL104
Escherichia coli PIR1 carrying pLL104 This paper PIR1 + pLL104
V. splendidus carrying transcriptional reporter plasmid pJAS2020.1 This paper 12B01 + pJAS2020.1
Escherichia coli PIR1 carrying pJAS2020.1 This paper PIR1 + pJAS2020.1
Escherichia coli DH5-alpha lambda pir carrying conjugative plasmid pEVS104 68 DH5-alpha lambda pir + pEVS104
Chemicals, peptides, and recombinant proteins
KpnI-HF NEB, Ipswich, MA, USA Cat#R3142
SphI NEB, Ipswich, MA, USA Cat#R3182
Chloramphenicol Sigma-Aldrich St. Louis, MO, USA Cat#C0378
Marine Broth BD, Franklin Lakes, NJ, USA Difco Cat# 2216
Low viscosity alginate Sigma-Aldrich St. Louis, MO, USA Cat#A1112
Alginate lyase Sigma-Aldrich St. Louis, MO, USA Cat#A1603
Ammonium chloride Sigma-Aldrich St. Louis, MO, USA Cat#213330
Nile Red Sigma-Aldrich St. Louis, MO, USA Cat#72485
Propidium Iodide Invitrogen Waltham, MA, USA Cat#P1304MP
Toto-3 Invitrogen Waltham, MA, USA Cat#T3604
Lysozyme Sigma-Aldrich St. Louis, MO, USA Cat#12650-88-3
15N-labeled ammonium, 99% Cambridge Isotope Laboratories, Tewksbury, MA, USA Cat#NLM-467-PK
16% Paraformaldehyde, aqueous, for electron microscopy Electron Microscopy Sciences, Hatfield, MA, USA Cat#50-980-487
Technovit 8100 resin Heraeus Kulzer GmbH Cat#64709012
Critical commercial assays
RNeasy kit Qiagen, Hilden, Germany Cat#74004
RNA Protect Bacterial Reagent Qiagen, Hilden, Germany Cat#76104
Lysing Matrix B MPBio, Santa Ana, CA, USA Cat#116911050-CF
Turbo RNA free DNAse kit Ambion, Austin, TX, USA Cat#AM1907
HS RNA screen tape Agilent, Santa Clara, CA, USA Cat#5067- 5579
HS RNA screen tape buffer Agilent, Santa Clara, CA, USA Cat#5067- 5580
HS RNA screen tape ladder Agilent, Santa Clara, CA, USA Cat#5067- 5581
Ribominus Yeast and Bacteria transcriptome isolation kit Invitrogen, Waltham, MA, USA Cat#A47335
TruSeq stranded mRNA-Seq kit Illumina, San Diego, CA, USA Cat#20020594
TruSeq indexes for paired end reads Illumina, San Diego, CA, USA Cat#PE-121-1003
Quant-iT RNA Assay kit Invitrogen, Waltham, MA, USA Cat#Q32884
Deposited data
12B01 genome assembly 77 NCBI Genome: ASM15276v1
RNASeq data This paper GEO: GSE190325
Github repostitory for image analysis code This paper78 N/A
Oligonucleotides
Pflp_SphI_F: CTTGCATGCTTACGATGCATAATAATTAGATTAGAAGTACCACAAAAAAG This paper N/A
Pflp_KpnI_R: TAGGTACCTTGCGTATCAGGCTTTGTTTACCTG This paper N/A
mKate_R_Seq: CTCTGAGGTGCACTTGA This paper N/A
8F: AGAGTTTGATCCTGGCTCAG 79 N/A
1492R: GGTTACCTTGTTACGACTT 79 N/A
pLL104_confirm_F:GGTGACCGGATCCTTACT This paper N/A
pLL103_confirm_F:TGACCGGATCCTCAACGG This paper N/A
pLL10X_confirm_R:ACTACGTTTCATAATGGTTATGAACTTT This paper N/A
Recombinant DNA
pLL103 65 N/A
pLL104 65 N/A
pJS2020.1 This paper N/A
pEVS104 68 N/A
Software and algorithms
Metamorph Molecular Devices, San Jose, CA, USA Version 6.2.3.733
ImageJ 80 Version 2.1.0/1.53h
Trimmomatic 81 Version 0.36
FastQC 82 Version 0.11.9
bbduk 73 Version 38.16
Bowtie2 83 Version 2.3.4.1
SAMTools 84 Version 1.9
HTSeq 85 Version 0.12.4
DeSeq2 86 Version 1.34.0
R Studio 87 Version 1.2.5042
TPM 74 N/A
Eggnogg mapper 88,89 Version 2.1
Look@nanosims 90 N/A
MATLAB Mathworks, Natick, MA, USA Release R2020b
Prism Graphpad, San Diego, CA, USA Version 9.3.1
Grid/collection ImageJ plugin 91 Version 1.2