Genomic DNA was prepared from overnight GBS cultures by a standard protocol for Gram-Positive bacteria, using Bacterial Genomic DNA kit (Takara Code NO.9164, Japan). Typing was performed by sequencing the internal fragments of seven house-keeping genes (adhP, pheS, atr, glnA, sdhA, glcK, and tkt). PCR was used to amplify genomic DNA using the primer pairs indicated at http://pubmlst.org/sagalactiae/info/primers.shtml . PCR products were purified and sequenced in both directions by BGI Tech Solutions Co. Ltd. Alleles and sequence types (STs) were determined using the S. agalactiae MLST website (http://pubmlst.org/sagalactiae/ ). Sequence types that shared five or more alleles of the seven loci were clustered into a clonal complex (CC) using eBURST software. The term “singleton ST” refers to an ST that did not cluster into a CC. BioNumerics software version 5.1 (Applied Maths, Belgium) was used to create minimum spanning trees to illustrate relationships between MLST and CCs.
Bacterial genomic dna kit
Manufactured by Takara Bio
Sourced in Japan
The Bacterial Genomic DNA Kit is a laboratory tool designed to efficiently extract and purify genomic DNA from bacterial samples. The kit utilizes a simple and optimized protocol to isolate high-quality DNA suitable for various downstream applications, such as PCR, sequencing, and molecular analysis.
Automatically generated - may contain errors
Lab products found in correlation
3 protocols using bacterial genomic dna kit
1
Multilocus Sequence Typing of Streptococcus agalactiae
2
Genomic Analysis of Strain TLK-CK17 T
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Genomic DNA of strain TLK-CK17 T was extracted and puri ed using a bacterial genomic DNA kit (Takara), following the manufacturer's recommendations. The taxonomic position of strain TLK-CK17 T was rst determined by 16S rRNA gene sequence using the primers XJ11 (5'-AGAGTTTGATCCTGGCTCAG-3') and XJ22 (5'-GGTTACCTTGTTACGACTT-3'). Whole-genome sequencing was performed on the Illumina HiSeq PE150 platform. A-tailed, ligated to paired-end adaptors and PCR ampli ed with a 350 bp insert was used for the library reconstruction. The raw reads were assembled using SOAPdenovo version 2.04 software (Li et al. 2008; Li et al. 2010 ). The genes of strain TLK-CK17 T were identi ed by NCBI Prokaryotic Genome Annotation Pipeline server online and the Pfam database (Angiuoli et al. 2008 ; http://pfam.xfam.org/), and the genes involved in metabolic pathways were analyzed in detail using the information present in RAST (Rapid Annotation using Subsystem Technology; https://rast.nmpdr.org). The G+C content of the chromosomal DNA was calculated using genome sequencing. The digital DNA-DNA hybridization (dDDH) values were calculated using the Genome-to-Genome Distance Calculator (GGDC 2.0) (Meier-Kolthoff et al. 2013). The average nucleotide identity (ANI) values were calculated using the algorithm of Goris et al. (Goris et al. 2007 ) by using the EzGenome web service.
3
Genomic Analysis of Strain TLK-CK17 T
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA of strain TLK-CK17 T was extracted and puri ed using a bacterial genomic DNA kit (Takara), following the manufacturer's recommendations. The taxonomic position of strain TLK-CK17 T was rst determined by 16S rRNA gene sequence using the primers XJ11 (5'-AGAGTTTGATCCTGGCTCAG-3') and XJ22 (5'-GGTTACCTTGTTACGACTT-3'). Whole-genome sequencing was performed on the Illumina HiSeq PE150 platform. A-tailed, ligated to paired-end adaptors and PCR ampli ed with a 350 bp insert was used for the library reconstruction. The raw reads were assembled using SOAPdenovo version 2.04 software (Li et al. 2008; Li et al. 2010 ). The genes of strain TLK-CK17 T were identi ed by NCBI Prokaryotic Genome Annotation Pipeline server online and the Pfam database (Angiuoli et al. 2008 ; http://pfam.xfam.org/), and the genes involved in metabolic pathways were analyzed in detail using the information present in RAST (Rapid Annotation using Subsystem Technology; https://rast.nmpdr.org). The G+C content of the chromosomal DNA was calculated using genome sequencing. The digital DNA-DNA hybridization (dDDH) values were calculated using the Genome-to-Genome Distance Calculator (GGDC 2.0) (Meier-Kolthoff et al. 2013). The average nucleotide identity (ANI) values were calculated using the algorithm of Goris et al. (Goris et al. 2007 ) by using the EzGenome web service.
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