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525
datasets available to search
ShareScore release 0.9.0
Dataset results
525 results for “Long reads”
HairSplitter: separating strains in metagenome assemblies with long reads
<p>Datasets, command lines and assemblies analyzed in the manuscript "HairSplitter: separating strains in metagenome assemblies with long reads".</p>
Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)
<p>Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.</p>
A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata)
<p><span>The sphinx moth genus <em>Hyles</em> comprises 29 described species inhabiting all continents except Antarctica. The genus diverged relatively recently (40 – 25 mya), arising in the Americas and rapidly establishing a cosmopolitan distribution. The whitelined sphinx moth, <em>Hyles lineata</em>, represents the oldest extant lineage of this group and is one of the most widespread and abundant sphinx moths in North America. <em>Hyles lineata </em>exhibits the large body size and adept flight control characteristic of the sphinx moth family (Sphingidae), but is unique in displaying extreme larval color variation and broad host plant use. These traits, in combination with its broad distribution and high relative abundance within its range, have made <em>H. lineata</em> a strong model organism for studying phenotypic plasticity, plant-herbivore interactions, physiological ecology, and flight control. Despite being one of the most well-studied sphinx moths, little data exists on genetic variation or regulation of gene expression. Here we report a high-quality draft genome showing high contiguity (N50 of 14.2 Mb) and completeness (98.2% of Lepidoptera BUSCO genes), an important first characterization to facilitate such studies. We also annotate the core melanin synthesis pathway genes and confirm that they have high sequence conservation with other moths and are most similar to those of another, well-characterized sphinx moth, the tobacco hornworm (<em>Manduca sexta</em>).</span></p>
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing
<p>Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium <em>Halotia branconii</em> CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.</p>
Long read isoforms with A-to-I edits for H1975 cell line
<p>FLAIR2 was used to determine isoform models sequenced from H1975 cells using R2C2 cDNA nanopore sequencing. RNA sequence variants observed in the data were called with longshot and integrated into FLAIR2 isoform models.</p>
HG002 data for Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing
<p>This dataset includes 6mA frequency data for the HG002 native DNA (untreated) sample sequenced on nanopore r9.4.1.</p>
NA12878 and MCF7 data for Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing
<p>This dataset includes 5mC and 6mA frequency data for NA12878 and MCF7 EcoGII-treated chromatin samples sequenced on nanopore r9.4.1.</p>
metaFlye: scalable long-read metagenome assembly using repeat graphs
<p>Supplementary files for the manuscript titled "metaFlye: scalable long-read metagenome assembly using repeat graphs".</p> <p>The archive includes generated assemblies and the corresponding metaQUAST evaluations.</p>
Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
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Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C
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Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
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A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata)
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Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
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Long-read-based draft genome sequence of Indian black gram IPU-94-1 ‘Uttara’: Insights into disease resistance and seed storage protein genes
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A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13
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Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing
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Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays
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De novo genome assembly of human cell line CHM13 nanopore ultra-long reads using Shasta
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Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease
<p>Supplemental File 1: Main genome assemblies (Unpolished Flye assembly, Polished Flye assembly, Unicycler Hybrid Assembly and Unicycler Illumina-only assembly) generated in this study for comparison and their BUSCO output.</p> <p>Supplemental File 2: Phyre2 protein modelling output of the putative MVP1 TcdA toxin</p> <p>Supplemental File 3: Phyre2 protein modelling output of the putative MVP1 TcdB toxin</p> <p>Supplemental File 4: Phyre2 protein modelling output of the putative MVP1 TccC toxin</p> <p>Supplemental File 5: InterProScan output of the NCBI-predicted MVP1 proteome.</p> <p>Supplemental Table 1: NCBI BlastN output using the <em>fuc</em> genes of <em>Vibrio parahaemolyticus</em> MVP1 as the query to search against the Vibrio reference WGS database as of 21 Oct 2019</p>
Nanopore raw signal data to Benchmarking the MinION: Evaluating long reads for microbial profiling
<p>This dataset contains original raw signal data of a blind study sequencing mock community samples. The samples are differing by nucleic acid quantification technique and composition, and consist of twelve prokaryotic species each. The raw signal data permits future basecalling and may assist in development of applications requiring signal level data.</p> <p>Sample 1 (Barcode 1): heterogenous, adjusted by ddPCR</p> <p>Sample 2 (Barcode 2): heterogenous, adjusted by Qubit</p> <p>Sample 3 (Barcode 3): equimolar, adjusted by ddPCR</p> <p>Sample 4 (Barcode 3): equimolar, adjusted by Qubit</p> <p>FLO-MIN106, SQK-LSK108; Flowcell FAH89600</p> <p>Please consider citing our paper</p> <p>Leidenfrost, R.M., Pöther, D., Jäckel, U. <em>et al.</em> Benchmarking the MinION: Evaluating long reads for microbial profiling. <em>Sci Rep</em> <strong>10, </strong>5125 (2020). https://doi.org/10.1038/s41598-020-61989-x</p> <p>https://doi.org/10.1038/s41598-020-61989-x</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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.