Characterization of a novel genus of jumbo phages and their application in wastewater treatment

. 2023 May 25;26(6):106947. doi: 10.1016/j.isci.2023.106947

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains

K. pneumoniae strains Kp9438	This paper	Kp9438
K. pneumoniae strains Kp5130	This paper	Kp5130
Phage φKp5130	This paper	φKp5130
Phage φKp9438	This paper	φKp9438
K. pneumoniae strains Kp 5137	This paper	Kp 5137
K. pneumoniae strains Kp 5619	This paper	Kp 5619
K. pneumoniae strains Kp 5295	This paper	Kp 5295
K. pneumoniae strains Kp 7338	This paper	Kp 7338
K. pneumoniae strains Kp 9088	This paper	Kp 9088
K. pneumoniae strains Kp 9194	This paper	Kp 9194
K. pneumoniae strains Kp 9385	This paper	Kp 9385
K. pneumoniae strains Kp 9502	This paper	Kp 9502
K. pneumoniae strains Kp 9947	This paper	Kp 9947
K. pneumoniae strains Kp 9841	This paper	Kp 9841
K. pneumoniae strains Kp 9856	This paper	Kp 9856
K. pneumoniae strains Kp 9310	This paper	Kp 9310
K. pneumoniae strains Kp 9349	This paper	Kp 9349
K. pneumoniae strains Kp 9498	This paper	Kp 9498
K. pneumoniae strains Kp 4547	This paper	Kp 4547
K. pneumoniae strains Kp 9773	This paper	Kp 9773
K. pneumoniae strains Kp 8860	This paper	Kp 8860
K. pneumoniae strains Kp 9298	This paper	Kp 9298
K. pneumoniae strains Kp 9816	This paper	Kp 9816
K. pneumoniae strains Kp 8372	This paper	Kp 8372
K. pneumoniae strains Kp 9628	This paper	Kp 9628

Chemicals, peptides, and recombinant proteins

PEG8000	SIGMA	P5413-2KG
DNase I	SIGMA	Cat # DN25
RNase A	Invitrogen	Cat # 12091021
Proteinase K	NEB	P8107S
LB Broth (Lennox)	Hopebio	HB0128
Agar	Sangon Biotech	A505255-0250
Sodium chloride (NaCl)	Sangon Biotech	A610476-0001
Magnesium Sulfate Heptahydrate (MgSO4 · 7H2O)	HUSHI	10013018
Trizma® Hydrochloride Solution (Tris-HCl)	SIGMA	T2694-1L
Gelatin	BBI	G9764-500g
Meropenem	Thermo Scientific	Cat#CT0774B
Cefoperazone	Thermo Scientific	Cat#CT0249B

Critical commercial assays

Norgen Phage DNA Isolation Kit	BIOTEK	Cat # 46800
Qubit™ dsDNA HS Assay Kit	INVITROGEN	Q32854
VITEK® 2 Gram Negative ID card (VITEK2 AST-GN13)	BioMérieux	Cat#22095

Deposited data

Assembly and annotation data of phages	China National GeneBank DataBase (CNGBdb)	https://ftp.cngb.org/pub/CNSA/data3/CNP0001966/
Raw data of phages	China National GeneBank DataBase (CNGBdb)	https://db.cngb.org/search/project/CNP0001966/

Software and algorithms

Fastp	Chen et al.²⁹	https://github.com/OpenGene/fastp
SOAPnuke	Chen et al.³⁰	https://github.com/BGI-flexlab/SOAPnuke
SPAdes	Bankevich et al.³¹	https://github.com/ablab/spades
prodigal	Hyatt et al.³²	https://github.com/hyattpd/Prodigal
BLASTp	Camacho et al.³³	https://blast.ncbi.nlm.nih.gov/Blast.cgi
hmmscan	Johnson et al.³⁴	https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan
tRNAscan-SE	Chan et al.³⁵	http://trna.ucsc.edu/tRNAscan-SE/
CGView	Stothard et al.³⁶	https://cgview.ca/
mafft	Katoh et al.³⁷	https://mafft.cbrc.jp/alignment/software/
IQ-TREE	Minh et al.³⁸	https://github.com/iqtree/iqtree2
iTOL	Letunic et al.³⁹	https://itol.embl.de/
vConTACT2	Bin Jang et al.⁴⁰	https://bitbucket.org/MAVERICLab/vcontact2/