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373
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ShareScore release 0.7.1
Dataset results
373 results for “Nanopore”
Peptide sequencing based on host-guest interaction-assisted nanopore sensing
<p>Source data files of "Peptide sequencing based on host-guest interaction-assisted nanopore sensing"</p>
nCNV-seq: nanopore-based CNV analysis tool for brain tumor classification & grading
<p>An available glioma test-dataset designed for nCNV-seq analysis and its corresponding database</p>
Peptide sequencing based on host-guest interaction-assisted nanopore sensing
<p>Source data for "Peptide sequencing based on host-guest interaction-assisted nanopore sensing"</p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 2
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 3
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
Evaluation of a mNGS Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.
ClinicalTrials.gov study NCT04864873. IPD Sharing: NO. Countries: 1. Publications: 12.
Application of Nanopore Adaptive Sequencing
ClinicalTrials.gov study NCT06542042. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: A first look at the Oxford Nanopore MinION sequencer
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Data for: Nanopore R10.4.1 LSK114 HG002: subset of 20000 reads in BLOW5 format
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Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
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Nanoporous copper and copper oxide with hollow microsphere structure prepared by polystyrene template-assisted synthesis
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Data from: Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer
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Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
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Data from: Nanopores in the ventral scales of Bitis rubida and Bitis armata cause white venters
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Data for: Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes
<p><span>Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) also brought about a large variety of assemblers. Although these have been extensively tested on model species such as <i>Homo sapiens </i>and <i>Drosophila melanogaster</i>, such benchmarking has not been done in Mollusca which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod <i>Chrysomallon squamiferum </i>(356.6Mb, 1.59% heterozygosity) and the bivalve <i>Mytilus coruscus</i> (1593Mb, 1.94% heterozygosity). By optimising the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by <i>C. squamiferum</i>, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by <i>M. coruscus</i>. A phylogenomic analysis utilising the two updated genomes with other 32 published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure the efficiency in future assemblies for molluscs and perhaps also other marine phyla with few genomes available.</span></p>
Data from: De novo sequencing and variant calling with nanopores using PoreSeq
The accuracy of sequencing single DNA molecules with nanopores is continually improving, but de novo genome sequencing and assembly using only nanopore data remain challenging. Here we describe PoreSeq, an algorithm that identifies and corrects errors in nanopore sequencing data and improves the accuracy of de novo genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA transits through the nanopore and finds the sequence that best explains multiple reads of the same region. PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 85% to 99% at 100× coverage. We also use the algorithm to assemble Escherichia coli with 30× coverage and the λ genome at a range of coverages from 3× to 50×. Additionally, we classify sequence variants at an order of magnitude lower coverage than is possible with existing methods.
Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
The red spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and Southeast Asia, and is a threatened species. The species is also considered a good model for studies of sex-inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single molecule sequencing and de novo assembly by Oxford Nanopore Technologies (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudo-chromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 non-coding RNAs. Furthermore, after mining several RNA-seq datasets, 23,809 (99.5%) genes were functionally annotated from a total of 23,924 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
Data for "A DNA turbine powered by a transmembrane potential across a nanopore"
<p>Data for "A DNA turbine powered by a transmembrane potential across a nanopore"</p>
Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore
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Can immature stages be ignored in studies of forest leaf litter arthropod diversity? A test using Oxford Nanopore DNA barcoding
<p>Datasets and results for the study</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.