REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Enzymes | ||
HaeIII | New England Biolabs (NEB) (Ipswich, MA, USA) | Cat# R0108S |
NgoIV | NEB | Cat# R0564S |
NlaIV | NEB | Cat# R0126S |
AsiSI | NEB | Cat# R0630S |
BamHI | NEB | Cat# R0136S |
NotI | NEB | Cat# R1089S |
SphI | NEB | Cat# R1082S |
PstI | NEB | Cat# R0140S |
BstUI | NEB | Cat# R0518S |
HaeII | NEB | Cat# R0107S |
SacI | NEB | Cat# R0156S |
NdeI | NEB | Cat# R0111S |
ClaI | NEB | Cat# R0197S |
SalI | NEB | Cat# R0138S |
PmeI | NEB | Cat# R0560S |
AseI | NEB | Cat# R0526S |
M.CviPI | NEB | Cat# M0227L |
M.SssI | NEB | Cat# M0226L |
DNAse I | Invitrogen (Carlsbad, CA, USA) | Cat# 18047019 |
Proteinase K | Sigma (St. Louis, MO,USA) | Cat# P2308 |
RNAse A | Qiagen (Hilden, Germany) | Cat# 19101 |
RNAse A, DNAse and protease-free | Thermo Fisher (Waltham, MA, USA) | Cat# EN0531 |
T4 ligase | Promega (Madison, WI, USA) | Cat# M0226L |
Phusion Polymerase | Thermo Fisher | Cat# F531L |
DNA Polymerase I Klenow Fragment | Promega | Cat# M2201 |
Bacterial strains (Table S1) | ||
E. coli (DH5α) | Lab collection | N/A |
E. coli Turbo Electrocompetent 5alpha | NEB | Cat# 2984H |
N. gonorrhoeae (MS11) | (Segal et al., 1985) | N/A |
ΔpilT | (Dietrich et al., 2009) | N/A |
ΔpilT/ipilT | This study | N/A |
ΔcomP | This study | N/A |
ΔcomP/comPWT | This study | N/A |
TD3 | This study | N/A |
N400 | (Tonjum et al., 1995) | N/A |
i35A | This study | N/A |
N. elongata | ATCC | N/A |
N. lactamica | ATCC | N/A |
N. cinerea | ATCC | N/A |
N. mucosa | ATCC | N/A |
N. sicca | ATCC | N/A |
N. polysaccharea | ATCC | N/A |
N. meningitidis | Lab collection | N/A |
Oligonucleotides | ||
Primers used for cloning and sequencing (Table S1) | This study | N/A |
DNA fragments (Table S1) | This study | N/A |
Plasmids | ||
pCR-Blunt | Thermo Fisher | Cat# K270020 |
pUC19 | AddGene (Watertown, MA, USA) | Cat# 50005 |
pBeloBAC11 | NEB | Cat# E4154 |
pKH37 | (Kohler et al., 2007) | N/A |
pNBNeiKan | (Weyand et al., 2016) | N/A |
pMR68 | (Ramsey et al., 2012) | N/A |
Growth Media | ||
GC medium base | Difco Laboratories Inc (Detroit, MI, USA) | Cat# 228920 |
GCB containing Kellogg’s Supplements I and II | (Kellogg et al., 1963) | N/A |
GCB containing vancomycin, colistin, nystatin | (Jacobs and Kraus, 1975) | N/A |
Glutaraldehyde | Electron Microscopy Sciences (EMS) (Hatfield, PA, USA) | Cat# 16000 |
Osmium tetroxide | EMS | Cat# 19100 |
Uranyl acetate | EMS | Cat# 22400 |
Chemicals | ||
IPTG | GoldBio (Olivette, MO, USA) | Cat# I2481C50 |
X-gal | Research Products International (RPI) (Mount Prospect, IL, USA) | Cat# B71800 |
S-adenosylmethionine (SAM) | NEB | Cat# B9003S |
BSA | Sigma | Cat# A2153 |
Ampicilin | GoldBio | Cat# 69523 |
Kanamycin | GoldBio | Cat# K120SL25 |
Erythromycin | Sigma | Cat# E5389 |
Chloramphenicol | Sigma | Cat# C0378 |
Vancomycin | RPI | Cat# V065500 |
Colistin | RPI | Cat# C70700 |
Nystatin | RPI | Cat# N82020 |
Ethanol | Sigma | Cat# 459836 |
Isopropanol | Sigma | Cat# I9516 |
Phenol | Sigma | Cat# 108952 |
Isoamyl alcohol | Sigma | Cat# 123513 |
Tissue Culture Plates | ||
Microplate dish (6-well) | Corning (Corning, NY, USA) | Cat# 0720083 |
Microplate dish (12-well) | Corning | Cat# 087721B |
Microplate dish (24-well) | Corning | Cat# 353847 |
Animal Model: Mice | ||
Female BALB/c (6-8 weeks old) | National Cancer Institute and Charles River (Jerse et al., 2011) | Cat# Strain_028 |
Other lab reagents | ||
0.22 μM PES Steriflip filter | Millipore (Burlington, MA, USA) | Cat# SE1M179M6 |
0.22 μM filter | Millipore | Cat# SLGV033RS |
Nucleobond Midi Columns | Macherey-Nagel (Düren, Germany) | Cat# 740410 |
Agarose | Sigma | Cat# A2576 |
Megabase Agarose | Bio-Rad (Hercules, CA, USA) | Cat# 1613108 |
Phase Lock Gels | VWR (Radnor, PA, USA) | Cat# 2302820 |
Gel Extraction Kit | Qiagen | Cat# 28706 |
Gel Extraction Kit | Thermo Fisher | Cat# K0691 |
Wizard Genomic DNA Purification Kit | Promega | Cat# A1120 |
Dacron Swabs | Thermo Fisher | Cat# 164KS01 |
CHEF Electrophoresis System | Bio-Rad | Cat# 1703670 |
Model 422 Electro-Eluter | Bio-Rad | Cat# 1652976 |
NanoDrop spectrophotometer | Thermo Fisher | RR_ID:SCR_015804 |
Software and algorithms | ||
Blastn | NCBI | RR_ID:SCR_007190 https://blast.ncbi.nlm.nih.gov/Blast.cgi |
GraphPad Prism 5.0 | GraphPad (San Diego,CA, USA) | RR_ID: SCR_002798 https://www.graphpad.com |
SMRT-Analysis | PacBio (Menlo Park, CA, USA) | RR_ID: SCR_002942 https://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ |
Quiver | (Chin et al., 2013) | N/A https://github.com/PacificBiosciences/GenomicConsensus |
Vim Text Editor | Vim | N/A https://www.vim.org/ |