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.
1,283
datasets available to search
ShareScore release 0.7.1
Dataset results
1,283 results for “Copying”
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
<p>In the paper associated with this dataset, a workflow is presented which enables the identification of single-/low-copy nuclear molecular markers for a plant group of interest, by mining data from a small representative target capture experiment done using a commercial probe kit and Oxford Nanopore long-read sequencing. The proposed pipeline first assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low-copy. The approach can be applied to any probe set. As it relies on long reads, the contribution also provides template workflows for processing Nanopore-based target capture data. Identified loci can be used for NGS amplicon sequencing. For detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, the long-read assembly tool CANU is employed. The presented workflow can be useful for researchers dealing with reticulate or polyploidization phylogenetic histories in plants.</p> <p>The present dataset contains several documents supplementing the original paper. Its most important elements are a detailed description (alongside two graphical workflow figures) of all methods employed in the study, suitable for reproducing the steps of the workflow and also the wet-lab work. The workflow employs a collection of BASH, Python and R scripts which is available here, together with a detailed account on command line use in Linux. Also, reference sequences for the identified markers can be found as well as sequence alignments derived from the amplicon sequencing.</p>
Copy number variations and their effect on the plasma proteome | Associations
<p>Results and supplementary data from a GWAS investigation the relationship of CNVs and blood protein measurements.</p>
Single-Dose Gene Replacement Therapy Using for Patients With Spinal Muscular Atrophy Type 1 With One or Two SMN2 Copies
ClinicalTrials.gov study NCT03837184. IPD Sharing: YES. Countries: 3. Publications: 1.
Pre-Symptomatic Study of Intravenous Onasemnogene Abeparvovec-xioi in Spinal Muscular Atrophy (SMA) for Patients With Multiple Copies of SMN2
ClinicalTrials.gov study NCT03505099. IPD Sharing: YES. Countries: 6. Publications: 3.
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
Open the record for dataset details and reuse information.
Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity
Open the record for dataset details and reuse information.
Data from: A social learning primacy trend in mate-copying; an experiment in Drosophila melanogaster
Open the record for dataset details and reuse information.
Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture
Open the record for dataset details and reuse information.
Prickly postglacial pioneers: freshwater plankton community composition influences fatty acid desaturase (FADS2) copy number in Southern Greenland threespine sticklebacks
Open the record for dataset details and reuse information.
Data from: A meta-analysis of factors influencing the strength of mate choice copying in animals
Davies et al., (2020) All data and R code <p>Mate-choice copying is a form of social learning in which an individual's choice of mate is influenced by the apparent choices of other individuals of the same sex, and has been observed in more than 20 species across a broad taxonomic range. Though fitness benefits of copying have proven difficult to measure, theory suggests that copying should not be beneficial for all species or contexts. However, the factors influencing the evolution and expression of copying have proven difficult to resolve. We systematically searched the literature for studies of mate-choice copying in non-human animals, and then performed a phylogenetically-controlled meta-analysis to explore which factors influence the expression of copying across species. Across 58 published studies in 23 species, we find strong evidence that animals copy the mate choice of others. The strength of copying was significantly influenced by taxonomic group, however sample size limitations mean it is difficult to draw firm conclusions regarding copying in mammals and arthropods. The strength of copying was also influenced by experimental design: copying was stronger when choosers were tested before and after witnessing a conspecific's mate choice, compared to when choosers with social information were compared to choosers without. Importantly, we did not detect any difference in the strength of copying between males and females, or in relation to the rate of multiple mating. Our search also highlights that more empirical work is needed to investigate copying in a broader range of species, especially those with differing mating systems and levels of reproductive investment.</p>
Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
<p>Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
Adaptation by copy number variation increases insecticide resistance in the fall armyworm (vcf files)
<p>Here, I deposite vcf files used for a paper, entitled 'Adaptation by copy number variation increases insecticide resistance in the fall armyworm'.</p> <p>genotype.vcf and SNP.filtered.vcf.gz have the information of CNVs and SNPs, respectively. </p>
Social learning by mate-choice copying increases dispersal and reduces local adaptation
<p class="MsoPlainText">1. In heterogeneous environments, dispersal may be hampered not only by direct costs, but also because immigrants may be locally maladapted. While maladaptation affects both sexes, this cost may be modulated in females if they express mate preferences that are either adaptive or maladaptive in the new local population.</p> <p class="MsoPlainText">2. Dispersal costs under local adaptation may be mitigated if it is possible to switch to expressing traits of locally adapted residents. In a sexual selection context, immigrant females may learn to mate with locally favoured males. Mate-choice copying is a type of social learning, where individuals, usually females, update their mating preferences after observing others mate. If it allows immigrant females to switch from maladapted to locally adapted preferences, their dispersal costs are mitigated as mate choice helps them create locally adapted offspring.</p> <p class="MsoPlainText">3. To study if copying can promote the evolution of dispersal, we created an individual-based model to simulate the coevolution of four traits: copying, dispersal, a trait relevant for local adaptation, and female preference. We contrast two scenarios with copying — either unconditional, or conditional such that only dispersers copy — with a control scenario that lacks any copying.</p> <p class="MsoPlainText">4. We show copying to lead to higher dispersal, especially if copying is conditionally expressed. This leads to an increase in gene flow between patches and, consequently, a decrease in local adaptation and trait-preference correlations.</p> <p class="MsoPlainText">5. While our study is phrased with female preference as the learned trait, one may generally expect social learning to mitigate dispersal costs, with consequent feedback effects on the spatial dynamics of adaptation.</p>
The cultural transmission of causally (ir)relevant actions in the laboratory: Does modelling or verbal instruction lead to greater copying fidelity?
<p>This study examines the fidelity with which adults vs. children transmit a set of actions within diffusion chains (generations 1 to 3). The set consisted of causally relevant and causally irrelevant actions. Half of the adult and half of the child chains transmitted the actions via demonstration (next participant saw the previous perform the actions on video); the other half transmitted them verbally (next participant listened to audio file the previous participant describe his/her actions). We measured whether the actions were retained (i.e. re-produced by each next participant in the chain).</p>
Koranic Science, a Copy of Kashshâf [IO Bijapur 275, 276, 277, 278]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 275, 276, 277, 278.</strong><strong>in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 54 here with further notations and hyperlinks]</strong>.</li> </ul> <p>54.</p> <p>B 275, 276, 277, 278. Size 12<sup>1/4</sup> in. by 7<sup>1/2</sup> in.; foll. 726. Twenty-six lines in a page.</p> <p>Another copy of the <em>Kashshâf</em>, including the whole text of the Koran. Well written. Dated Shawwal, 921.<sup>1</sup></p> <p>This MS. Has been spoiled by damp. It has also many defects, which were supplied in a later hand; but since then a number of leaves of both sets have again fallen out. Originally in four volumes. The first concludes with Sûrah 6 (fol. 184); the second with Sû. 18 (fol. 376); the third with Sû. 38 (fol. 559<em>v.</em>). The beginning of the fourth, being in the second hand, is on the same page.</p> <p>Catal. p. 219, i.</p> <p> </p> <p><sup>1</sup> The beginning of the colophon, containing the name of the scribe, has been erased.</p>
Koranic Science, a Copy of Kashshâf [IO Bijapur 282, 283]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 282, 283 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 57 here with further notations and hyperlinks]</strong>.</li> </ul> <p>57.</p> <p>B 283, 282. Size 12<sup>3/4</sup> in. By 6<sup>1/2</sup> in.; foll. 251. Twenty-three lines in a page.</p> <p>الربع الرابع من تفسیر الکشاف عن حقائق التنزیل مؤلف الامام العلامة ذی الشان الجلیل استاذ الدنیا شیخ العرب و العجم حجة الاسلام و قدوة اهل العالم ابی القاسم محمود بن عمر الزمخشریّ البسه الله تعالی لباس الغفران و رزقه الاتکآء علی رفرفٍ خُضر و عبقریّ آمین بالنّبی الامین<sup>1</sup>.</p> <p>The last quarter of the <em>Kashshâf</em>; beginning with Sû. 18. Beautifully written, of about the eighth century. Rubrics sometimes omitted. At the end the author’s epilogue. In two volumes, the first ending with Sû. 48 (fol. 99). Both the beginning and (in a less degree) the end are injured by damp.</p> <p> </p> <p><sup>1</sup> This inscription was written on the title-page in Rabî’ I., 921. The name of the owner who wrote it has been erased.</p> <p> </p>
Koranic Science, a Copy of Kashshâf [IO Bijapur 281]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 281 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 56 here with further notations and hyperlinks]</strong>.</li> </ul> <p>56.</p> <p>B 281. Size 11 in. by 7<sup>1/4</sup> in.; foll. 230. Twenty-five lines in a page.</p> <p>The third quarter of the <em>Kashshâf, </em>comprising Sûrah 19-37.</p> <p>Beautifully written, of about the ninth century. The final portion, however, has been supplied in a more modern hand.</p> <p>The first leaf and the last but one are wanting. Much injured by insects.</p> <p> </p>
Koranic Science, a Copy of Kashshâf [IO Bijapur 287]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 287 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 59 here with further notations and hyperlinks]</strong>.</li> </ul> <p> </p> <p>59.</p> <p>B 287. Size 10<sup>1/2</sup> in. by 6<sup>3/4</sup> in.; foll. 501. Twenty-seven lines in a page.</p> <p>The last part of a voluminous Super-commentary on the <em>Kashshâf</em>, by Sharȧf aldîn al-Ḥusain b. Muḥammad ṬAIYBÎ, (d. A. H. 743), from Sû. 35 to the end. Cf. Ḥ. Kh. v. 185, and Flügel, Hdss. Wien, iii., 74.</p> <p>Beginning: قوله و عن ابن عباس ما کنت ادری ما فاطر السموات. Written in Nasta’lîḳ, of about the tenth century. Various defects, and the whole final portion, have been supplied in another, indifferent handwriting. One leaf, containing the end of the author’s epilogue, is missing at the end. Injured at the beginning.</p> <p>Cat. p. 221, i. 8 (?).</p> <p> </p>
Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. Variation at RLG1a was associated with multiple traits in pooled population resequencing (PoolSeq) scans of phenotypic and phenological cohorts. Five of 35 (14%) of resequenced inbred lines carried three-copy variants of RLG1a (trip+), and trip+ lines exhibited elevated RLG1a expression. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (P < 0.05). In early-flowering wild cohorts, we discovered an additional rare variant (high+) that carries 250-300 copies of RLG1a totaling ~5.7Mb, equivalent to 20-40% of a chromosome. Mendelian segregation of diagnostic alleles and qPCR-based copy counts In the progeny of a high+ carrier, indicate that high+ is a single tandem array unlinked from the single copy RLG1a locus in the reference genome. In the wild, high+ carriers had highest fitness in two dry and/or hot years (2015 and 2017; both P < 0.01), while single copy individuals were twice as fecund as either CNV genotype in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
<p><span><span><span><span><span><span><span><span><span><span><span>The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. Here, we explain this association by elucidating a mutational cascade, downstream of <a>th</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>e single cell division error of chromosome bridge formation, that rapidly generates extreme genomic complexity. We show that actomyosin forces are required for initial bridge breakage and mutagenesis, following which chromothripsis accumulates with aberrant interphase replication of bridge DNA. This is then followed by an unexpected burst of DNA replication in the next mitosis, generating extensive DNA damage. During this second cell division, broken bridge chromosomes frequently mis-segregate and form micronuclei, promoting additional chromothripsis. We <a>fu</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>rther show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.</span></span></span></span></span></span></span></span></span></span></span></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.