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.
3,696
datasets available to search
ShareScore release 0.9.0
Dataset results
3,696 results for “reference”
Fig 1 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 1. Bat species with recent (dated during or after the year 2000) and old (dated before year 2000) records from Peninsular Malaysia. https://doi.org/10.1371/journal.pone.0179555.g001
Reference allele frequencies for populations pools of Atlantic Herring (Clupea harengus)
<p>Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.</p>
PdO reference
<a href="https://spectroscopyhub.com/measurements/5699f839-15c7-4b4d-98ca-4f10fb36e50a">PdO reference</a>
reference spectra of Ag0.98Pd0.02 and Ag0.95Pd0.05
<a href="https://spectroscopyhub.com/measurements/data-collection/c2f3f5e0-de45-4df2-9f2e-3110b632573e">reference spectra of Ag0.98Pd0.02 and Ag0.95Pd0.05</a>
Pd metal reference
<a href="https://spectroscopyhub.com/measurements/84678ccc-f81a-4546-97fe-c4175fb8fce1">Pd metal reference</a>
Data from: Loci contributing to boric acid toxicity in two reference populations of Drosophila melanogaster
Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3–188), allowing us to identify plausible candidate genes underlying resistance to boric acid toxicity. One interval contains multiple genes from the cytochrome P450 family, and we show that ubiquitous RNAi of one of these genes, Cyp9b2, markedly reduces resistance to the toxin. Resistance to boric acid is positively correlated with caffeine resistance. The two phenotypes additionally share a pair of QTL, potentially suggesting a degree of pleiotropy in the genetic control of resistance to these two distinct xenobiotics. Finally, we screened the Drosophila Genetic Reference Panel (DGRP) in an attempt to identify sequence variants within mapped QTL that are associated with boric acid resistance. The approach was largely unsuccessful, with only one QTL showing any associations at QTL-specific 20% False Discovery Rate (FDR) thresholds. Nonetheless, these associations point to a potential candidate gene that can be targeted in future validation efforts. Although the mapping data resulting from the two reference populations do not clearly overlap, our work provides a starting point for further genetic dissection of the processes underlying boric acid toxicity in insects.
Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3' end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.
Data from: Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as "Tilapia"
African cichlids formerly referred to as "Tilapia" represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important "Tilapia" or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for "Tilapia" joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.
Data from: GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome
Genotyping-by-sequencing (GBS) and related methods are increasingly used for studies of non-model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double-digest RAD, GBS, and two-enzyme GBS without a reference genome. GIbPSs can handle paired-end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality for data filtering and export in numerous formats. We performed comparative analyses of simulated and real GBS data with GIbPSs and another program, pyRAD. This program accounts for indel variation by aligning homologous sequences. GIbPSs performed better than pyRAD in several aspects. It required much less computation time and displayed higher genotyping accuracy. GIbPSs retained smaller numbers of loci overall in analyses of real GBS data. It nevertheless delivered more complete genotype matrices with greater locus overlap between individuals and greater numbers of loci sampled in all individuals.
Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.
Data from: The association between alcohol consumption, cardiac biomarkers, left atrial size and re-ablation in patients with atrial fibrillation referred for catheter ablation
Background: Information on alcohol consumption in patients undergoing radiofrequency ablation (RFA) of atrial fibrillation (AF) is often limited by the reliance on self-reports. The aim of this study was to describe the long-term alcohol consumption, measured as ethyl glucuronide in hair (hEtG), in patients undergoing RFA due to AF, and to examine potential associations with cardiac biomarkers, left atrial size and re-ablation within one year after the initial RFA. Methods: The amount of hEtG was measured in patients referred for RFA, and a cut-off of 7 pg/mg was used. N-terminal pro B-type natriuretic peptide (NT-proBNP) and the mid-regional fragment of pro atrial natriuretic peptide (MR-proANP) were examined and maximum left atrium volume index (LAVI) was measured. The number of re-ablations was examined up to one year after the initial RFA. Analyses were stratified by gender, and adjusted for age, systolic blood pressure, body mass index, presence of heart failure and heart rhythm for analyses regarding NT-proBNP, MR-proANP and LAVI and heart rhythm being replaced by type of AF for analyses regarding re-ablation. Results: In total, 192 patients were included in the study. Median (25th – 75th percentile) NT-proBNP in men with hEtG ≥ 7 vs. < 7 pg/mg was 250 (96-695) vs. 130 (49-346) pg/ml (p = 0.010), and in women it was 230 (125-480) vs. 230 (125-910) pg/ml (p = 0.810). Median MR-proANP in men with hEtG ≥ 7 vs. < 7 pg/mg was 142 (100-224) vs. 117 (83-179) pmol/l (p=0.120) and in women it was 139 (112-206) vs. 153 (93-249) pmol/l (p = 0.965). The median of maximum LAVI was 30.1 (26.7-33.9) vs. 25.8 (21.4-32.0) ml/m2 (p = 0.017) in men, and 25.0 (18.9-29.6) vs. 25.7 (21.7-34.6) ml/m2 (p =0.438) in women, with hEtG ≥ 7 vs. < 7 pg/ml, respectively. Adjusted analyses showed similar results, except for MR-proANP turning out significant in men with hEtG ≥ 7 vs. < 7 pg/mg (p=0.047). The odds ratio of having a re-ablation was 3.5 (95% CI 1.3-9.6, p = 0.017) in men with hEtG ≥ 7 vs. < 7 pg/mg, while there was no significant difference in women. Conclusions: In male patients with AF and hEtG ≥ 7 pg/mg, NT-proBNP and MR-proANP were higher, LA volumes larger, and there was a higher rate of re-ablations, as compared to men with hEtG < 7 pg/mg. This implies that men with an alcohol consumption corresponding to an hEtG-value ≥ 7, have a higher risk for LA remodelling that could potentially lead to a deterioration of the AF situation.
Data from: Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs
Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods living fossil species which have existed on the earth for 500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome-level T. tridentatus genome, and proofed that this genome is of very high quality with contig N50 1.69 Mb. By comparison with other arthropods, some gene families of T. tridentatus experienced significant expansion, whichare related to several signaling pathways, endonuclease activity, and metabolic processes. Based on the comparative analysis of genomics and 27 transcriptomes from 9 tissues, we found that the expanded Dscam genes usually locate at the key hub positions of immune network. Furthermore, the Dscam genes showed higher levels of expression in the yellow connective tissue, the birthplace of blood cells with strong differentiation capability, than the other 8 tissues. Besides, Dscam genes are positively correlated with the expression of the core immunity gene, clotting factor B, which is implicated in the coagulation cascade reaction. The effective and unusual immune ability endowed by the expansion and expression of Dscam genes in horseshoe crabs may be a factor that makes horseshoe crabs having a strong environmental adaptability with ~500 million years. The high-quality chromosome-level genome of a horseshoe crab and unique genomic features reported in this study provide important data resources for future studies on the evolutionary history of marine ecological systems.
Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
The red spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and Southeast Asia, and is a threatened species. The species is also considered a good model for studies of sex-inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single molecule sequencing and de novo assembly by Oxford Nanopore Technologies (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudo-chromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 non-coding RNAs. Furthermore, after mining several RNA-seq datasets, 23,809 (99.5%) genes were functionally annotated from a total of 23,924 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
FIGURE 4 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 4. Title page of volume 4 of the Histoire Naturelle. Insectes. Laporte separate edition.
FIGURE 2 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 2. Timeline of production for all the dictionnaires of the EM.
FIGURE 14 in The Cholevinae of Romania (exclusive of Leptodirini) (Coleoptera, Leiodidae) with special reference to the hypogeal records
FIGURE 14. Distribution of Catops tristis, C. ventricosus and C. nitidicollis in Romania.
FIGURE 10 in The Cholevinae of Romania (exclusive of Leptodirini) (Coleoptera, Leiodidae) with special reference to the hypogeal records
FIGURE 10. Distribution of Catops picipes in Romania.
FIGURE 7 in The Cholevinae of Romania (exclusive of Leptodirini) (Coleoptera, Leiodidae) with special reference to the hypogeal records
FIGURE 7. Distribution of Choleva nivalis, Ch. oresitropha and Ch. reitteri in Romania.
FIGURE 15 in The Cholevinae of Romania (exclusive of Leptodirini) (Coleoptera, Leiodidae) with special reference to the hypogeal records
FIGURE 15. Distribution of Catops subfuscus in Romania.
FIGURE 1 in The Cholevinae of Romania (exclusive of Leptodirini) (Coleoptera, Leiodidae) with special reference to the hypogeal records
FIGURE 1. Distribution of Anemadus strigulosus and Nemadus colonoides in Romania.
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.