For this study, the whole genomes of 80 S. mutans isolates that were obtained from the supragingival dental plaque of children in Bengbu, China, were preserved in our laboratory and were sequenced and assembled (see Table S4 in the supplemental material). A TIANamp bacteria DNA kit (Tiangen Biotech, Beijing, China) was used for bacterial genomic DNA (gDNA) isolation based on provided directions, after which 1 μg of DNA from each sample was used with a NEBNext Ultra DNA library prep kit for Illumina (NEB, USA) in order to prepare libraries for sequencing. Barcodes were added to each sample during this process. Samples were then sonicated into 350-bp fragments, followed by end polishing, poly(A) tail processing, ligation to full-length Illumina adaptors, and additional PCR amplification. The AMPure XP system was then used to extract the amplified libraries, which were subjected to quality control analysis and quantification using an Agilent 2100 Bioanalyzer and via real-time PCR. An Illumina NovaSeq 6000 PE150 instrument was then used to sequence these 80 whole genomes at Novogene Bioinformatics Technology (Beijing, China), and the SOAPdenovo software was used for sequence assembly.
Novaseq 6000 pe150 instrument
Manufactured by Illumina
Sourced in China, United States
The NovaSeq 6000 PE150 is a high-throughput sequencing instrument designed for large-scale genomic studies. It can perform paired-end sequencing with read lengths up to 150 base pairs. The instrument is capable of generating a large volume of sequencing data to support a variety of applications, including whole-genome sequencing, exome sequencing, and transcriptome analysis.
Automatically generated - may contain errors
Lab products found in correlation
Nebnext ultra dna library prep kit, by Illumina (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Tianamp bacteria dna kit, by Tiangen Biotech (1 mentions)
Lt sample prep kit, by Illumina (1 mentions)
Trizol, by Takara Bio (1 mentions)
Pt l2p, by DNA Genotek (1 mentions)
Twist human core exome capture kit, by Twist Bioscience (1 mentions)
3 protocols using novaseq 6000 pe150 instrument
1
Whole Genome Sequencing of S. mutans Isolates
2
Transcriptomic Profiling of LV-siAUP1 Cells
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Total RNA was extracted from LV‐NC and LV‐siAUP1 cells using TRIzol (TAKARA) and further treated with DNase to remove genomic DNA contamination. An RNA library was constructed using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), and then the RNA‐seq library was sequenced using an Illumina NovaSeq 6000 PE150 instrument by Haplox Biotechnology Co.
3
Whole Exome Sequencing for Genetic Profiling
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Genomic DNA was extracted from saliva samples using the prepI-L2P protocol, according to the manufacturer's instructions (PT-L2P, DNA Genotek). Whole exome sequencing (WES) was performed for the probands of the three families (MAPK1960, MAPK1243, and PK106-5) using the Twist Human Core Exome Capture Kit (Twist Bioscience, San Francisco, CA, USA) and an Illumina NovaSeq 6000 PE150 instrument (Illumina, San Diego, CA, USA).
Reads were aligned to the human reference genome (hg19/ GRCH37) using the NovoAlign software (V3.08.00; Novocraft Technologies). Duplicate reads were identified with MarkDuplicates (Picard) [15] . We used the genome analysis toolkit GATK (v3.8) [16] for single base quality score and recalibration, Exo-meDepth (v2.1) [17] to detect copy number variations, and HaplotypeCaller [18] to generate VCF files containing all the variants. Furthermore, AutoMap [19] was used to identify runs of homozygosity (ROHs) from WES data, and an in-house developed in silico bioinformatics pipeline was applied for variant annotation and filtration [20] .
Reads were aligned to the human reference genome (hg19/ GRCH37) using the NovoAlign software (V3.08.00; Novocraft Technologies). Duplicate reads were identified with MarkDuplicates (Picard) [15] . We used the genome analysis toolkit GATK (v3.8) [16] for single base quality score and recalibration, Exo-meDepth (v2.1) [17] to detect copy number variations, and HaplotypeCaller [18] to generate VCF files containing all the variants. Furthermore, AutoMap [19] was used to identify runs of homozygosity (ROHs) from WES data, and an in-house developed in silico bioinformatics pipeline was applied for variant annotation and filtration [20] .
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