Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,023
datasets available to search
ShareScore release 0.9.0
Dataset results
1,023 results for “copy number”
Simulated data and results from "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data"
<p>This dataset contains all the simulated data and the results of all the considered methods in the benchmark presented in "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data" [Zaccaria & Raphael, 2018]. All the data in this dataset and the corresponding formats are fully described at <a href="https://github.com/raphael-group/hatchet-paper">https://github.com/raphael-group/hatchet-paper</a>. The folder <em>simulations</em> which contains the entire dataset has been compressed with standard <em>zip</em>.</p>
Copy Number variants in Mallotus villosus
<p>Taking advantage of recent developments allowing CNV analysis from RAD-seq data (<a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15565?_sg%5B0%5D=-uwA9TZisRRXnspI5ElYUaPv2ChLuHLDZPIJZABoML2rc-geS2mVnZVIt2u4FAB6_SPD-DeRxtzyN3RjHivkmfmvEg.JqPMUYewJwfNoZvoALtl54UTEL4BWYI0NA87y3HrK16wm8cRVOG0c0owiV4QoaSysHfAZCLPkLmn-UaqCdolJQ">10.1111/mec.15565</a>), we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (<i>Mallotus villosus</i>). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. Raw sequencing data for GBS libraries have been published in a previous study (Cayuela et al. 2020, <a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15499?_sg%5B0%5D=OGdqMkvPArx5ICrgLrdT_ifFufXzoOZp0J7gLQEctL4EWpJv-h9FK8yFaom_h68N368lpxVYXRREN9BRpAi7lH0n8A.ylPnOWuObAEr1NJn9bzfYxNNAAwvYDvN0jDBR05xnfdW8Azf-PmnI7jDZFhecO1Kt1aTdFuxG0Yr3ff2e10XCg">10.1111/mec.15499</a>) and are available under accession no. PRJNA631144. Here, we provide the files of normalized read depth for the 6620 putative CNVs and environmental data used in our CNV analyses.</p>
Data from: Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita
Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, e.g., resistant hosts. Here we used a genome-wide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals.
Data from: The cost of copy number in a selfish genetic element: the 2µM plasmid of Saccharomyces cerevisiae
Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2µm is a multi-copy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2µm is that plasmid copy number evolves as a tradeoff between selection for increased vertical transmission, favoring high copy number, and selection for decreased virulence, favoring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2µm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (±0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast/2µm associations, and pave the way for future studies examining how selection can shape the cost of multi-copy elements.
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional divergence. We investigated the evolutionary relationship of the LRR-RLK gene family by phylogenetic analysis and found that these closely related paralogs resulted from multiple duplication events, such as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify gene expression changes in immature anthers from the bam1/bam2 single and double mutants compared with wild type providing strong evidence that the BAM1 and BAM2 genes have evolved different functions, with differential effects on anther gene expression. Moreover, careful examination of anther development in bam1 and bam2 single mutants revealed previously unrecognized extra cell division in tapetum cell layers. Thus our results from phylogenetic, molecular and morphological analyses uncover sequence and functional differences between paralogs whose single mutants lack obvious fertility defects, effectively revealing functional divergence of duplicate genes.
Gene copy number is associated with phytochemistry in Cannabis sativa
<p>Gene copy number variation is known to be important in nearly every species where it has been examined. Alterations in gene copy number may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. <i>Cannabis sativa </i>plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids -THCA and CBDA - are products of a three-step biochemical pathway. Using whole genome shotgun sequence data for 69 <i>Cannabis</i> cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in copy number. Transcriptome sequence data shows that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that copy number partially explains variation in cannabinoid content levels among <i>Cannabis</i> plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped copy number variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.</p>
Data from: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1.
Sample site coordinates, environmental data, number of copies of target DNA/ul for each sample and limit of detection plot
<p>Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly-disparate systems. As upper trophic level predators, bull sharks (<i>Carcharhinus leucas</i>) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama suggest that bull sharks extensively use the northern portions of the bay, an estuarine-freshwater interface known as the Mobile-Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 x<span> 1</span> L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile-Tensaw Delta, and ten sites throughout the Mobile-Tombigbee and Tensaw-Alabama Rivers. Water samples were vacuum-filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species-specific primers and an internal probe to amplify a 237-base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less urbanized, riverine habitats up to 120 km upriver during Alabama's dry summer season.</p>
Supplementary material 2 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 2
Supplementary material 1 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 1
Supplementary material 3 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 3
Supplementary material 4 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Tables S1–S4, Figures S1–S4
Dataset for "Association between Amylase Alpha 1 Gene (AMY1) Copy Number Variation and Dental Caries Experience in Turkish Population"
Open the record for dataset details and reuse information.
Data from: Cyanobacteria maintain constant protein concentration despite genome copy-number variation
The cyanobacterium Synechococcus elongatus PCC 7942 has multiple copies of its single chromosome, and the copy number varies in individual cells, providing an ideal system to study the effect of genome copy-number variation on cell size and gene expression. Using single-cell fluorescence imaging, we found that protein concentration remained constant across individual cells regardless of genome copy number. Cell volume and the total protein amount from a single gene were both positively, linearly correlated with genome copy number, suggesting that changes in cell volume play an important role in buffering genome copy-number variance. This study provides a quantitative examination of gene expression regulation in cells with variable genome copies and sheds light on the compensation mechanisms for variance in genome copy number.
Copy number aberrations segmentfile
<p>Copy number aberrations. Segmentfile.</p>
Data from: Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer
Open the record for dataset details and reuse information.
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Open the record for dataset details and reuse information.
Data from: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants
Open the record for dataset details and reuse information.
Gene copy number is associated with phytochemistry in Cannabis sativa
Open the record for dataset details and reuse information.
Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum
Open the record for dataset details and reuse information.
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.