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.
71
datasets available to search
ShareScore release 0.9.0
Dataset results
71 results for “Nuclear loci”
Data from: Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci
Open the record for dataset details and reuse information.
Data from: Development of nuclear microsatellite loci and mitochondrial single nucleotide polymorphisms for the natterjack toad, Bufo (Epidalea) calamita (Bufonidae), using next generation sequencing and Competitive Allele Specific PCR (KASPar)
Open the record for dataset details and reuse information.
Data from: Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa
Open the record for dataset details and reuse information.
Data from: Despite introgressive hybridization, North American birches (Betula spp.) maintain strong differentiation at nuclear microsatellite loci
Open the record for dataset details and reuse information.
12 nuclear microsatellite loci scores for 543 adult trees of Tilia cordata in Lithuainia
Open the record for dataset details and reuse information.
Genotypes of Swan Geese Anser cygnoides using 17 nuclear microsatellite loci at 14 locations.
Open the record for dataset details and reuse information.
Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Open the record for dataset details and reuse information.
Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes
Open the record for dataset details and reuse information.
Data from: Molecular phylogeny of Tragopogon L. (Asteraceae) based on seven nuclear loci (Adh, GapC, LFY, AP3, PI, ITS, and ETS)
Open the record for dataset details and reuse information.
Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci
Open the record for dataset details and reuse information.
Data from: High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography
One of the major challenges for researchers studying phylogeography and shallow-scale phylogenetics is the identification of highly-variable and informative nuclear loci for the question of interest. Previous approaches to marker generation have generally required extensive testing of loci of unknown utility from other systems or development of markers from the nearest model organism with genomic resources. Here, we present a fast and economical approach to generating thousands of variable, single-copy nuclear loci for any system using next-generation sequencing. We performed Illumina paired-end sequencing of three reduced-representation libraries (RRLs) in chorus frogs (Pseudacris) to identify orthologous, single-copy loci across libraries and to estimate sequence divergence at multiple taxonomic levels. We also conducted PCR testing of these loci across the genus Pseudacris and outgroups to determine whether loci developed for phylogeography can be extended to deeper phylogenetic levels. Prior to sequencing, we conducted in silico digestion of the most closely-related reference genome (Xenopus tropicalis) to generate expectations for the number of loci and degree of coverage for a particular experimental design. Using the RRL approach, we: (1) identified >100,000 single-copy nuclear loci, 6,339 of which were shared across individuals within species and 904 of which were shared between species, (2) estimated average nuclear sequence divergence at 0.1% between alleles within an individual, 1.1% between conspecific individuals, and 1.8% between species, and (3) determined from PCR testing that 53% of the loci successfully amplify within-species and also many amplify to the genus-level and beyond (16%). Our study effectively identified nuclear loci present in the genome that have levels of sequence divergence on par with mitochondrial markers commonly used in phylogeography. Specifically, we estimated that ~7% of loci in the chorus frog genome are >3% divergent within species; this translates to ~50,000 single-copy loci in the genome with >3% divergence. Moreover, successful amplification of many loci at deeper phylogenetic levels indicates that the RRL approach represents an efficient method for rapid generation of informative markers for both phylogenetics and phylogeography. We conclude by making recommendations for minimizing the cost and maximizing the efficiency of marker development for future studies in this field.
Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.
Data from: Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families
Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships
<p>Multiple Sequence DNA alignments of the Angiosperm353 target enrichment loci and their corresponding ML gene tree phylogenies</p>
FIGURE 2 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
FIGURE 2. Species-coalescence tree of the orchid family inferred from 292 maximum likelihood (ML) gene trees. Pie diagrams at nodes represent quartet support values, with q1 (deep blue portion) representing the proportion of gene tree quartets that support the main (depicted) branch, q2 (blue portion) representing the proportion of quartets supporting the first alternative branch, and q3 (gray portion) representing the proportion of quartets supporting the second alternative branch (an explanation of how the quartet values are computed is available at https://github.com/smira rab/ASTRAL/blob/master/astral-tutorial.md). (Inset): ML tree derived from a supermatrix of 292 low copy nuclear genes. Terminal names with alternative positions to those obtained by the species-tree coalescence analysis are highlighted in bold and red. Adetailed version of the tree is presented in Appendix S4.
Data from: Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families
Open the record for dataset details and reuse information.
Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci
Open the record for dataset details and reuse information.
Data from: High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography
Open the record for dataset details and reuse information.
Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci
GEO Series GSE148396. Homo sapiens. 29 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Genome variation profiling by SNP array; SNP genotyping by SNP array.
Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [ATAC-seq]
GEO Series GSE176421. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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.