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.
281
datasets available to search
ShareScore release 0.9.0
Dataset results
281 results for “copy number variation”
Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients
Open the record for dataset details and reuse information.
Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
Open the record for dataset details and reuse information.
Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
Open the record for dataset details and reuse information.
Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation
Open the record for dataset details and reuse information.
Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
Open the record for dataset details and reuse information.
Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
Open the record for dataset details and reuse information.
Amaranthus palmeri EPSPS copy number and glyphosate resistance variation
Open the record for dataset details and reuse information.
Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
Open the record for dataset details and reuse information.
Avian MHC copy number variation is associated with helminth richness
<p>Genes of the Major Histocompatibility Complex (MHC) play a key role in the adaptive immunity of vertebrates, as they encode receptors responsible for recognition of antigens. Evolutionary history of the MHC proceeded through numerous gene duplications, which increases the spectrum of pathogens recognized by individuals. Although pathogen-mediated selection is believed to be a primary driver of MHC expansion over evolutionary times, empirical evidence for this association is virtually lacking. Here, we used an extensive dataset on MHC class II copy number variation in non-passerine birds to test for an evolutionary correlation with helminth parasite richness. As expected, our phylogenetically-informed modelling revealed a positive association between MHC copy number and total helminth richness, even after controlling for a broad spectrum of ecological and life-history traits. Thus, total helminth richness appears to be the most important correlate of MHC copy number, supporting a leading role of pathogen-mediated selection in the evolution of MHC in birds. Our results provide some of the first, although correlative, evidence linking parasitism to inter-specific variation in MHC copy number among birds.</p>
NanoString nCounter copy number variation assay
<p>The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies, and the W chromosome has been largely overlooked. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the W both across and within avian species. We find a striking deficit of gene families on the duck W chromosome, as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Furthermore, we show that gene families have expanded independently in the duck and chicken. In particular, using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors, we investigate the factors driving the expansion of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. While we find that HINTW is ampliconic in both species, our results support a role of female-specific selection in driving gene amplification in the chicken but not the duck, challenging the assumption that HINTW is key for female fecundity across the avian phylogeny.</p>
Data from: Distribution and functionality of copy number variation across European cattle populations
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
Data from: Dynamics of copy number variation in host races of the pea aphid
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Grs and Ors, respectively), in the process of host race formation. We used targeted re-sequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors, and a decrease in the probability of complete gene duplication or deletion (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Grs were over-represented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
NanoString nCounter copy number variation assay
Open the record for dataset details and reuse information.
Data from: Copy number variation and expression analysis reveals a nonorthologous pinta gene family member involved in butterfly vision
Open the record for dataset details and reuse information.
Avian MHC copy number variation is associated with helminth richness
Open the record for dataset details and reuse information.
Data from: Dynamics of copy number variation in host races of the pea aphid
Open the record for dataset details and reuse information.
Data from: Distribution and functionality of copy number variation across European cattle populations
Open the record for dataset details and reuse information.
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.
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.
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.