Long-read nanopore sequencing of a pancreatic cancer cell culture derived from a KPC mouse.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39427 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4351540_1.fastq.gz | Fastqsanger.gz | |||
| ERR4351539_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Linkage of genetic drivers and strain-specific germline variants confound mouse cancer genome analyses
| PRJEB39429 | ENA
Project description:Linkage of genetic drivers and strain-specific germline variants confound mouse cancer genome analyses
| PRJNA646626 | ENA
Project description:The integration of long-read sequencing technology, such as nanopore sequencing technology [Oxford Nanopore Technologies (ONT)], into routine diagnostic laboratories has the potential to transform bacterial infection diagnostics and improve patient management. Analysis of amplicons from long-read sequencing of the 16S rRNA gene generates a comprehensive view of the microbial community within clinical samples, significantly enhancing sensitivity and capacity to analyse mixed bacterial populations compared to short read sequencing approaches. This study evaluates various ONT sequencing approaches and library preparation kits to establish a reliable testing and quality framework for clinical implementation. This study highlights the critical importance of using well-characterized reference materials in validating and revalidating long-read sequencing methods, leveraging a combination of standardized reference materials and clinical samples to navigate the evolving landscape of microbial diagnostics. It presents a robust validation framework for laboratory accreditation and outlines a methodology for comparing the performance of newer ONT chemistries with earlier versions. Additionally, the study details the methods and quality control measures necessary for achieving more accurate and efficient diagnoses of bacterial infections, ultimately reducing time to treatment and enhancing patient outcomes.
| S-EPMC11922894 | biostudies-literature
Project description:The nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA) molecules as examples, we demonstrate the superior accuracy of basecallers trained by our scheme.
| S-EPMC11429927 | biostudies-literature
Project description:Unveiling the potential application of psychrophilic polymerases as candidates for polymerase-nanopore long-read sequencing presents a departure from conventional choices such as thermophilic Bacillus stearothermophilus (Bst) renowned for its limitation in temperature and mesophilic Bacillus subtilis phage (phi29) polymerases for limitations in strong exonuclease activity and weak salt tolerance. Exploiting the PB-Bst fusion DNA polymerases from Psychrobacillus (PB) and Bacillus stearothermophilus (Bst), our structural and biochemical analysis reveal a remarkable enhancement in salt tolerance and a concurrent reduction in exonuclease activity, achieved through targeted substitution of a pivotal functional domain. The sulfolobus 7-kDa protein (Sso7d) emerges as a standout fusion domain, imparting significant improvements in PB-Bst processivity. Notably, this study elucidates additional functional sites regulating exonuclease activity (Asp43 and Glu45) and processivity using artificial nucleotides (Glu266, Gln283, Leu334, Glu335, Ser426, and Asp430). By disclosing the intricate dynamics in exonuclease activity, strand displacement, and artificial nucleotide-based processivity at specific functional sites, our findings not only advance the fundamental understanding of psychrophilic polymerases but also provide novel insights into polymerase engineering.
| S-EPMC11246872 | biostudies-literature
Project description:This experiment aims to define the transcriptome of pea cultivars, and find differences between cultivars and between epigenetic wild-type and \"rogue\" plants.
2025-02-28 | E-MTAB-14841 | biostudies-arrayexpress
Project description:RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
| S-EPMC9723614 | biostudies-literature
Project description:BackgroundThe MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, the output of which could be used to benchmark analysis tools.ResultsHere, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim.ConclusionIn this work, we model the base-calling errors of ONT reads to inform the simulation of sequences with similar characteristics. We showcase the performance of NanoSim on publicly available datasets generated using the R7 and R7.3 chemistries and different sequencing kits and compare the resulting synthetic reads to those of other long-sequence simulators and experimental ONT reads. We expect NanoSim to have an enabling role in the field and benefit the development of scalable next-generation sequencing technologies for the long nanopore reads, including genome assembly, mutation detection, and even metagenomic analysis software.
| S-EPMC5530317 | biostudies-literature
Project description:Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies-based long-read sequencing "nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers. The Galaxy platform provides a user-friendly interface to computational command line-based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed "NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads. A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
| S-EPMC7568507 | biostudies-literature
Project description:Bulk RNA sequencing of sorted peri-pancreatic LN cDC1s from different stages of neoplastic development in the KPC mouse model of pancreatic adenocarcinoma.
2020-04-15 | GSE126361 | GEO