Project description:Long-read RNA sequencing is a powerful technology for transcriptomics, but low throughput and high cost pose challenges. Adaptive sampling, a feature of Oxford Nanopore Technologies, offers real-time enrichment by selectively ejecting non-target molecules. We evaluate adaptive sampling for human transcriptome analysis.
Project description:We used targeted long-read Oxford Nanopore Technologies sequencing enriching for a panel of 1036 pharmacogenes extracted from the PharmGKB database. The enrichment was performed using ONT's adaptive sampling feature, enabling in silico enrichment without physically capturing the fragments of interest using hybridization.
Project description:We generated Oxford Nanopore long-read RNA-seq data to compare transcript isoform usage across four primate species and two cell types. We profiled induced pluripotent stem cells (iPSCs) and iPSC-derived neural precursor cells (NPCs) from human (Homo sapiens), gorilla (Gorilla gorilla), orangutan (Pongo abelii), and cynomolgus macaque (Macaca fascicularis).
Project description:Genome-wide 5-methylcytosine (5mC) profiling at CpG dinucleotides in Hydra viridissima using Oxford Nanopore long-read sequencing with Dorado base modification detection. Five ONT runs (one symbiotic, four aposymbiotic clone 2) were basecalled with Dorado sup,5mCG_5hmCG, aligned to Carnegie v1 genome assembly (JBWVZK000000000), and methylation quantified with modkit. Global CpG methylation is ~9-10%, bimodal (88% unmethylated, 7% fully methylated). Unique genomic regions show higher methylation (12%) than repetitive regions (7.5%).
Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
2021-12-03 | GSE179673 | GEO
Project description:Species identification of mammalian scat using nanopore adaptive sampling