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.
33
datasets available to search
ShareScore release 0.9.0
Dataset results
33 results for “linking elements”
Limno-STOICH a comprehensive database linking the elemental content of organisms with inland, aquatic habitats (2025-12-11)
The Limnology Stoichiometric Traits of Organisms In their Chemical Habitats (Limno-STOICH) contains >51,000 observations of organismal elemental content fro >3,100 rivers, lakes, wetlands, and other aquatic ecosystem sites on seven continents. The data are derived from 190+ sources including author contributed collections, novel NEON-related data, and published datasets. The database also includes extensive spatial and temporal metadata to link elemental stoichiometry with ecosystem type, trophic status, etc., and information on organismal data (body size, taxonomic classifications, stable isotope composition) and water physicochemical parameters, as available. Users are encouraged to read the associated manuscript (Corman et al.) for further information.
Geochemistry and petrography of martian meteorite Northwest Africa 11115: A rare earth element-enriched olivine-phyric shergottite closely linked to Northwest Africa 1068
<p>This is the Electronic Appendix of the manuscript "<strong>Geochemistry and petrography of martian meteorite Northwest Africa 11115: A rare earth element-enriched olivine-phyric shergottite closely linked to Northwest Africa 1068</strong>", by M. Melwani Daswani, N. Greber, J. Hu, R. C. Greenwood, and P. R. Heck, submitted to <em>Meteoritics & Planetary Science</em>.</p> <p>Corresponding author: M. Melwani Daswani (daswani@jpl.caltech.edu)</p> <p>The compressed folder contains two files:</p> <p>1) <strong>NWA11115_CT_scan_TIFF_substack.tif</strong></p> <p>This is a TIFF image stack of the CT scan of the full NWA 11115 sample. Open in a program such as ImageJ (Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, <a href="https://imagej.nih.gov/ij/">https://imagej.nih.gov/ij/</a>, 1997-2018).</p> <p>2) <strong>NWA11115_CT_scan_60FPS_JPEG.avi</strong></p> <p>This is a video file of the CT scan of the same NWA 11115 sample. The TIFF stack was converted to a video file (.avi), compressed to JPEG quality, and at a rate of 60 frames per second. Open this file with software such as VLC (<a href="https://www.videolan.org/vlc/">https://www.videolan.org/vlc/</a>).</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>The authors acknowledge T. Boudreaux for donating NWA 11115 to the Field Museum, J. Greer and J. Holstein for help with sample preparation, L. Kööp and B. Strack for SEM support, S. Rastegar for preliminary SEM analysis, L. Dussubieux for LA-ICP-MS support, A. I. Neander and Z.-X. Luo for CT scanning and support, and J. Filiberto and A. Treiman for useful discussions. We thank Thomas Pettke for assistance with LA-ICP-MS analyzes of the pressed powder pellets at the University of Bern. GPS Division analytical facilities at Caltech and Chi Ma are thanked for the support on EMPA analysis. PRH acknowledges support from the Tawani Foundation. MMD’s portion of the work was done partly as a private venture and not in the author’s capacity as an employee of the Jet Propulsion Laboratory, California Institute of Technology. The authors declare no competing interests.</p> <p>EOF</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Visualizing phage infection
<p>We staged infections at four multiplicities of infection (MOI 0, 0.01, 0.1, and 1), and took snapshots every ten minutes over a 40-minute period. We designed FISH probes targeting the non-coding strand of the <em>gp34</em> gene, which encodes a tail fiber protein and quantified cells with 5 or more MGE spots, less than 5 spots, and no spots</p>
Dataset: The plural interpretability of German linking elements ("Morphology")
<p><strong>This dataset accompanies a paper to be published in "Morphology" (JOMO, Springer). Under the present DOI, all data generated for this research as well as all scripts used are stored. The paper itself is not CC-licensed, refer to Springer's "Morphology" website for details!</strong></p> <p><strong>Abstract</strong></p> <p>In this paper, we take a closer theoretical and empirical look at the linking elements in German N1+N2 compounds which are identical to the plural marker of N1 (such as <em>-er</em> with umlaut, as in <em>Häus-er-meer</em> 'sea of houses'). Various perspectives on the actual extent of plural interpretability of these pluralic linking elements are expressed in the literature. We aim to clarify this question by empirically examining to what extent there may be a relationship between plural form and meaning which informs in which sorts of compounds pluralic linking elements appear. Specifically, we investigate whether pluralic linking elements occur especially frequently in compounds where a plural meaning of the first constituent is induced either externally (through plural inflection of the entire compound) or internally (through a relation between the constituents such that N2 forces N1 to be conceptually plural, as in the example above). The results of a corpus study using the DECOW16A corpus and a split-100 experiment show that in the internal but not external plural meaning conditions, a pluralic linking element is preferred over a non-pluralic one, though there is considerable inter-speaker variability, and limitations imposed by other constraints on linking element distribution also play a role. However, we show the overall tendency that German language users do use pluralic linking elements as cues to the plural interpretation of N1+N2 compounds. Our interpretation does not reference a specific morphological framework. Instead, we view our data as strengthening the general approach of probabilistic morphology.</p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity
<p>We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH
<p>We used <em>Escherichia coli </em>transformed with pJKR-H-tetR plasmids encoding an inducible <em>GFP</em> gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the <em>GFP</em> gene, used non-transformed <em>E. coli </em>as a negative control, and tested six different FISH protocols.<strong> </strong></p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping
<p>We used rRNA FISH to stain five common oral genera, <em>Veillonella, Streptococcus, Corynebacterium, Lautropia, </em>and <em>Neisseria</em>, each with a different fluorophore, and we used MGE-FISH to stain the <em>termL</em> gene of an active prophage with a sixth fluorophore. </p> <p>We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump. </p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
Open the record for dataset details and reuse information.
Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.
Data from: A selfish genetic element linked to increased lifespan impacts metabolism in female house mice
Gene drive systems can lead to the evolution of traits that further enhance the transmission of the driving element. In gene drive, one allele is transmitted to offspring at a higher frequency than the homologous allele. This has a range of consequences, which generally include a reduction in fitness of the carrier of the driving allele, making such systems <i>selfish</i>. The t haplotype is one such driver, found in house mice. It is linked to a reduction in litter size in matings among heterozygous animals, but also to increased lifespan in wild females that carry it. Here, we tested whether carrying the t haplotype was associated with altered resting metabolic rate (RMR). We show that females carrying the t haplotype decrease RMR as they increase in size, compared to wildtype females or males of either genotype. Our study elucidates a plausible mechanism by which a selfish genetic element increases lifespan.
Data from: Altered leaf elemental composition with climate change is linked to reductions in photosynthesis, growth and survival in a semiarid shrubland
Climate change will increase heat and drought stress in many dryland areas, which could reduce soil nutrient availability for plants and aggravate nutrient limitation of primary productivity. Any negative impacts of climate change on foliar nutrient contents would be expected to negatively affect the photosynthetic capacity, water use efficiency and overall fitness of dryland vegetation. We conducted a four-year manipulative experiment using open top chambers and rainout shelters to assess the impacts of warming (~2ºC, W), rainfall reduction (~30%, RR) and their combination (W+RR) on the nutrient status and ecophysiological performance of six native shrub species of contrasting phylogeny in a semiarid ecosystem. Leaf nutrient status and gas exchange were assessed yearly, whereas biomass production and survival were measured at the end of the study. Warming (W and W+RR) advanced shoot growth phenology and reduced foliar macro- (N, P, K) and micronutrient (Cu, Fe, Zn) concentrations (by 8-18% and 14-56%, respectively), net photosynthetic rate (32%), aboveground biomass production (28-39%) and survival (23-46%). Decreased photosynthesis and growth in W and W+RR plants was primarily linked to enhanced nutritional constraints on carbon fixation. Poor leaf nutrient status in W and W+RR plants partly decoupled carbon assimilation from water flux and led to drastic reductions in water use efficiency (WUEi; ~41%) across species. The RR treatment moderately decreased foliar macro- and micronutrients (6-17%, except for Zn) and biomass production (22%). The interactive impacts of warming and rainfall reduction (W+RR treatment) on plant performance were generally smaller than expected from additive single‐factor effects. Synthesis: Large decreases in plant nutrient pool size and productivity combined with increased mortality during hotter droughts will reduce vegetation cover and nutrient retention capacity, thereby disrupting biogeochemical processes and accelerating dryland degradation with impending climate change. Increased macro- and micronutrient co-limitation of photosynthesis with forecasted climate change conditions may offset any gains in WUEi and productivity derived from anthropogenic CO2 elevation, thereby increasing dryland vegetation vulnerability to drought stress in a warmer and drier climate. The generalized reduction in leaf nutrient contents with warming compromises plant nutritional quality for herbivores, with potential cascading negative effects across trophic levels.
Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Open the record for dataset details and reuse information.
Data from: Altered leaf elemental composition with climate change is linked to reductions in photosynthesis, growth and survival in a semiarid shrubland
Open the record for dataset details and reuse information.
Data from: A selfish genetic element linked to increased lifespan impacts metabolism in female house mice
Open the record for dataset details and reuse information.
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin. [Activation of stellate cells by tumor conditioned medium]
GEO Series GSE134093. Homo sapiens. 6 samples. Type: Expression profiling by array.
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin
GEO Series GSE161956. Homo sapiens. 13 samples. Type: Methylation profiling by high throughput sequencing.
Link between GRHL2 Motifs and Intratumor Heterogeneity of Cis-Regulatory Elements Results in Poor Outcome in Luminal Breast Cancer: A Single-cell Chromatin Accessibility Analysis
GEO Series GSE198639. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cellular trajectory analysis links tissue maturation to cellular specialization in the plant meristem [protophloem sieve element cells]
GEO Series GSE142259. Arabidopsis thaliana. 21 samples. Type: Expression profiling by high throughput sequencing.
The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1–linked chromatin opening
GEO Series GSE223050. Mus musculus. 336 samples. Type: Expression profiling by high throughput sequencing; 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.