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660 results for “genome assembly”
Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
<p>The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species' demographic history should be considered. Furthermore, we provided compelling evidence of selection through the examination of allele frequency changes over time, by taking into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low and decreasing levels of genetic diversity. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.</p>
Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries
<p>Upload of relevant sequencing data for the paper "<strong>Cell-free synthesis of infective phages from <em>in vitro</em> assembled phage genomes for efficient phage engineering and production of large phage libraries"</strong></p>
High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations
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Transcript- and annotation-guided genome assembly of the European starling
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Data from: Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases
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Chromosome-level genome assembly and annotation of the emblematic silver-lipped pearl oyster, Pinctada maxima Jameson, 1901
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The genome assemble of Bemisia tabaci MED
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Automated improvement of stickleback reference genome assemblies with Lep-Anchor software
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Data for: Highly contiguous genome assembly of Drosophila prolongata – a model for evolution of sexual dimorphism and male-specific innovations
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A chromosome-level genome assembly of the beavertail cactus, Opuntia basilaris
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Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
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Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
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Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
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Kellet's whelk genome and transcriptome assembly
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Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi
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Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation
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The LakePulse Metagenome-Assembled Genome catalogue
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Raw Nanopore data for "Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia, and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga"
<p>This is the raw Nanopore dataset (fast5) for Hydrogenophaga intermedia PBC. The gDNA was prepared using the now obsolete SQK-NSK007 kit and sequenced on a MINION R9 Flowcell. </p>
Dataset for "Nanopore-led long-read genome assembly of the Australian yabby, Cherax destructor"
<p>Intermediate_Assemblies.tar.gz: Intermediate genome assemblies e.g. raw wtdbg assembly (CD.raw.fa), polished wtdbg assembly (CD.cns.fa), 1st pilon polished assembly (CDF2_pilon1.fasta), 2nd pilon polished assembly (CDF2_pilon2.fasta) and RNA-scaffolded assembly (CDF2_pilon2_prna.fasta). Folders with run_"assembly name" are BUSCO output for each of the assembly.</p> <p>BRAKER2.tar.gz: BRAKER2 genome annotation output containing the initial set of predicted protein-coding genes as well as training intermediate files.</p> <p>BUSCOv3.tar.gz: BUSCO assessment of publicly available Decapod crustacean genome assemblies</p> <p>Cdes.filtered.codingseq: Filtered set of protein-coding sequences</p> <p>Cdes.filtered.faa: Translation of the filtered protein-coding sequences</p> <p>CDF2.NCBI.fasta.masked.gz: Repeat-masked (softmasked) Cherax destructor genome</p> <p>Cqua_transcriptome.tar.gz: rnaSPAdes output (combined fasta) of all Cherax quadricarinatus transcriptomes and its reduced dataset generated by EvidentialGene. </p> <p>Quast.tar.gz: Quast output of all Decapod crustacean genome assemblies assessed in this study</p> <p>Repeat_Annotation.tar.gz: Repeat annotation (.gff3) based on Cherax destructor-specific de novo repeat library and its summary (.tbl)</p> <p>RepeatLibrary.tar.gz: Cherax destructor-specific de novo repeat library generated by RepeatModeler</p> <p>Wtdbg2_assembly.log: Wtdbg2.5 log file showing exact command used, kmer distribution, memory usage and assembly duration.</p> <p>CAZY_Annotation.tar.gz: dbCAN2 Identification of CAZy in the selected crustacean proteomes as well as list of cellulase-associated GH groups (glycoside hydrolase). </p> <p>Orthofinder.tar.gz: Orthofinder2 output and proteomes of each crustacean used to infer orthologous clustering.</p> <p>GH9_Analysis.tar.gz: Selected GH9-associated protein sequences, amino acid alignment and IQTree output. </p> <p>Cdes_mito.gbf: GenBank file of the annotated complete mitogenome</p> <p>Cdes.filtered.codingseq: Cherax destructor protein-coding genes with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.filtered.faa: Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.ortholog.list: List of predicted Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p>
Whole genome assembly and gene annotation of a diploid genotype of Brachiaria ruziziensis (syn. Urochloa ruziziensis)
<p>In this work, we have presented a comprehensive analysis of the molecular mechanism linked to aluminium tolerance in <em>Brachiaria</em> species. By assembling and annotating a diploid genotype of <em>B. ruziziensis</em> we have developed the capability for genomic-based studies of desirable phenotypic traits. Using this resource, we have identified three QTLs associated to root architecture and vigour during Al<sup>3+</sup> stress in a hybrid population from a high and low tolerant accession. We have also identified a number of genes and molecular responses that impact on different aspects of signalling, cell-wall composition and active transports as a response to aluminium stress. <em>Brachiaria </em>tolerance appears to build in the same genes than in rice. However, we found that external mechanisms such as sequestration of Al<sup>3+</sup> common in other grasses might be not that important in <em>Brachiaria. </em>Also, contrasting regulation in the same genotype after 8 or 72 hours of Al<sup>3+</sup> stress of numerous genes involved in RNA translation can explain the different levels of tolerance among different Brachiaria species. The newly annotated draft genome represents an important base upon which study other aspects of <em>Brachiaria</em> biology.</p>
ScienceDex guides
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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.