In total, 1,263 WGS sequencing data were obtained from BioProject PRJEB31846 . The dataset comprises diverse S. enterica serovars collected between the years 1999 and 2019 and sequenced by the National Reference Laboratory for Salmonella using the Nextera XT or DNA Flex kit (Illumina GmbH, München, Germany) on Illumina MiSeq and NextSeq instruments. The data are described in more detail in (Uelze et al., 2019 ).
Dna flex kit
Manufactured by Illumina
Sourced in Germany
The DNA Flex kit is a laboratory instrument designed for DNA isolation and purification. It utilizes automated magnetic bead-based technology to extract high-quality DNA from a variety of sample types. The kit provides a streamlined and efficient process for obtaining DNA samples suitable for downstream applications.
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Lab products found in correlation
8 protocols using dna flex kit
1
Comprehensive Salmonella Genomic Dataset
2
NGS Sequencing of Yeast Mutants
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Genomic DNA of isolated mutants, parental strain and population samples were extracted using YeaStar DNA extraction kit (Zymo Research). Library preparations and NGS sequencing were performed by the Texas A&M Genomics Center for sequencing on the Illumina MiSeq platform using 300 × 300 paired-end reads using Nexterra DNAFlex kit for library generation. An average coverage of > 20-fold was obtained for each isolated mutant and > 150-fold for population samples. The sequencing data was aligned to S. cerevisiae S288c reference genome with breseq v0.29 [42 (link)]. De novo mutations in isolated mutants were identified by comparing against the YAG113 parental strain, and verified via Sanger sequencing. The raw sequencing data were deposited in SRA database (https://www.ncbi.nlm.nih.gov/sra ) with accession number PRJNA669136.
3
Single-Cell RNA-Seq Analysis Pipeline
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Library was prepared using Illumina DNA flex kit by the Sequencing and Bioinformatics Consortium at the University of British Columbia, following the manufacturer’s protocol. In library preparation, we used a custom P5 adapter along with a custom read primer for read1 to read out from the custom site. The prepared library was sequenced using Nextseq 550 with High output, 25 bp READ1(custom) and 125 bp READ2. After sequencing, the UMI was detected using UMI-tools, and then the poly-A tail was removed using Cutadapt. The trimmed fastq file was aligned and mapped using Hisat2 aligner against GRCh38 from NCBI, along with RefSeq annotation. The aligned BAM file was fed into featureCounts in Subread package to count the number of UMI detected per gene. Since featureCounts create BAM tags XT for each gene, and XS for assigned status, we used these tags in count function of UMI-tools to count and deduplicate the reads. Further statistic analyze was performed using edgeR package in R.
4
Validating iSeq 100 with MiSeq
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To validate the iSeq 100 results, the same iSeq 100 libraries were used for MiSeq deep sequencing. Nine samples were selected, at least one from each iSeq 100 run, making sure not to use the same i5 and i7 tags. These nine libraries were sent to the Animal Disease Diagnostic Laboratory (Ohio Department of Agriculture, Reynoldsburg, Ohio) for sequencing. Library preparation was performed using an Illumina DNA Flex kit, and 2 × 250 sequencing was performed on the MiSeq platform using V3 chemistry. The pipeline described above was used to analyze the MiSeq fastq files.
5
Klebsiella pneumoniae Genomic Analysis
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DNA was extracted from bacterial isolates using the Qiagen EZ1 tissue kit (Qiagen, Hilden, Germany) extraction method according to manufacturer’s instructions. Sequencing libraries were prepared using the Illumina DNA Flex kit (Illumina, San Diego, CA) and sequencing was performed on the Illumina MiSeq instrument (Illumina, San Diego, CA) using 2 x 250 protocol. Genomic analysis was done using the KmerFinder, ResFinder, Multi Locus Sequence Typing (MLST), and PlasmidFinder tools provided by the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/ ). Additional analyses of sequence data were performed using CLC Genomics Workbench v12.0.3 (Qiagen, Hilden, Germany) and Geneious Prime software (Biomatters, Auckland, New Zealand), including mapping, de novo assembly, and variant analysis. Sequence data was mapped to the following references: Klebsiella pneumoniae strain KP38731, complete genome (Genbank NZ_CP014294.1), and Klebsiella pneumoniae plasmid pKPS30, complete sequence (Genbank NC_023314.1).
6
Bacterial Genome Sequencing and Assembly
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Genomic DNA was extracted from an overnight bacterial culture using the DNeasy Blood and Tissue Mini Kit (QIAGEN GmbH, Germany) according to the manufacturer’s protocol. A standard genomic library was prepared from the DNA using the Illumina DNA Flex Kit (Illumina) and sequenced using the Illumina MiSeq platform (2 × 300 bp, paired end). Quality control and assembly were performed as described previously.11 (link)
Briefly, raw sequences were trimmed for quality using Sickle 1.33 (parameters: q > 30 and l > 45).12 The cleaned sequences were then assembled using SPAdes 3.13.0 using the option --careful and --only-assembler.13 (link) Contigs obtained from the assembly were curated for length (>1000 bp) and coverage (>10×) to minimize errors and contamination in the draft genome. Annotation was performed using Prokka 1.14.1 (based on Genetic Code Table 11).14 (link) Assembled genome data are available from the NCBI GenBank under the BioProject numberPRJNA604888 . Raw read data are available upon request. Sequencing statistics are summarized in Table S1 (available as Supplementary data at JAC Online).
Briefly, raw sequences were trimmed for quality using Sickle 1.33 (parameters: q > 30 and l > 45).12 The cleaned sequences were then assembled using SPAdes 3.13.0 using the option --careful and --only-assembler.13 (link) Contigs obtained from the assembly were curated for length (>1000 bp) and coverage (>10×) to minimize errors and contamination in the draft genome. Annotation was performed using Prokka 1.14.1 (based on Genetic Code Table 11).14 (link) Assembled genome data are available from the NCBI GenBank under the BioProject number
7
Illumina Nextera Flex DNA Sequencing
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The Illumina library was prepared using the Nextera Flex DNA kit. The library was sequenced on an SP flow cell (14%) of the Illumina Nova Seq 6000 sequencing platform (Ramaciotti Centre, University of New South Wales, Australia) using the paired-end protocol to produce 112 million 150-bp reads in pairs, an estimated 43× genome coverage. The median insert size was 713 bp.
8
Nextera Flex DNA Sequencing Protocol
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Illumina library was prepared using the Nextera Flex DNA
kit. The library was sequenced on an SP flow cell (14%) of the Illumina Nova Seq 6000 sequencing platform (The Ramaciotti Centre, University of New South Wales, Australia) using the paired-end protocol to produce 112 million 150 bp reads in pairs, an estimated 43× genome coverage. The median insert size was 713 bp.
kit. The library was sequenced on an SP flow cell (14%) of the Illumina Nova Seq 6000 sequencing platform (The Ramaciotti Centre, University of New South Wales, Australia) using the paired-end protocol to produce 112 million 150 bp reads in pairs, an estimated 43× genome coverage. The median insert size was 713 bp.
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