Novaseq 6000 platform
The NovaSeq 6000 platform is a high-throughput sequencing system designed for large-scale genomic studies. It utilizes the latest sequencing-by-synthesis (SBS) technology to generate high-quality sequencing data. The platform can be used to perform a variety of applications, including whole-genome sequencing, exome sequencing, and transcriptome analysis.
Lab products found in correlation
27 protocols using novaseq 6000 platform
RNA Sequencing Library Preparation
Single-cell RNA-seq of Megakaryocytes
Bacterial Species Identification via WGS
Transcriptome Analysis of Insect Salivary Glands
ChIP-seq Analysis of Histone H3K27 Acetylation
Rumen Microbiome Analysis by 16S Sequencing
The singletons and chimeras were removed, and then tags were clustered into the operational taxonomic unit (OTU) using UPARSE (V 7.0.1001,
Linear discriminant analysis coupled with effect size (LEfSe) was conducted to identify bacterial taxa differentially represented among the groups at various taxonomy levels. An LDA effect size of more than 2.5 was used as threshold for the LEfSe analysis.
Whole-Genome Sequencing of Onion Bacterial Strains
Gut Microbiome DNA Extraction and Sequencing
Microbiome bioinformatics were performed with QIIME2 2021.4.47 (link) Shannon index for alpha diversity and Bray-Curtis for beta diversity measures. Principle Coordinate Analysis (PCoA) were analyzed using the vegan v2.5–7 R package. Taxonomy was assigned to ASVs using the qiime feature-classifier classify-sklearn. Naive Bayes classifiers trained on Silva 138 99% OTUs from 515 F/806 R region of sequences. Gene functions analysis were predicted as previous method.48 (link) Predicted functions were calibrated for all of samples (n = 73) using Meta-Apo49 (link) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Thirty paired metagenomic samples were used for training.
Metagenomic Sequencing and Functional Profiling
Raw sequence reads were trimmed using Trimmomatic v0.39 to remove adapters and low-quality regions and then removed of contaminating human reads using Bowtie2 v2.4.2 (Reference database: GRCh38).50 (link) The taxonomic composition was profiled using the default parameters of MetaPhlAn3 v3.0.9.51 (link) The functional gene pathway was profiled using the default settings of HUMAnN3 v3.0.0.alpha.3.52 (link) Functional potential profiling of microbial communities was performed by HUMAnN3 using pangenomes annotated with UniRef90 on all species detectable per sample with MetaPhlAn3. Functional annotations rely on the MetaCyc database and gut-brain modules (GBMs) database.
ChIP-Seq Analysis of H3K27ac in NB4 Cells
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