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ShareScore release 0.9.0
Dataset results
354 results for “data access”
Modeling gene regulation from matched expression and chromatin accessibility data
GEO Series GSE98479. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
GEO Series GSE109828. Homo sapiens. 32 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Time course regulatory analysis based on paired expression and chromatin accessibility data
GEO Series GSE136312. Mus musculus. 54 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [RNA-Seq]
GEO Series GSE219011. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
Chromatin-accessibility estimation from single-cell ATAC data with scOpen
GEO Series GSE139950. Homo sapiens; Mus musculus. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Chili pepper RNA-Seq data for fruit development in a set of accessions
GEO Series GSE165448. Capsicum annuum. 179 samples. Type: Expression profiling by high throughput sequencing.
Single-cell chromatin accessibility data using scATAC-seq
GEO Series GSE65360. Homo sapiens; Mus musculus. 1632 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
KDM3B suppresses APL Progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα (RNA-seq data set)
GEO Series GSE137104. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Single-cell chromatin accessibility data from K562 cells using scATAC-seq
GEO Series GSE99172. Homo sapiens. 288 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide chromatin accessibility data from cultured human fetal lung tip-derived organoids at different stages of lung development
GEO Series GSE178527. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
INTERFLEX - EON (SWE) open access data
<p>Open access data for backing up results presented by EON within the Interflex-project.</p>
Data supplement for: "Open Access für die Maschinen"
<p>Structured bibliographical metadata for the paper: "Open Access für die Maschinen".</p>
Extended data for publication "Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies"
<p>This archive contains the extended data for the publication "Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies". This includes two sheet within the "ExtendedData.xlsx" file:</p> <p>Table1: List of all functions available in DODO R package with description and scope details.<br> Table2: List of ontologies among which the cross-reference relations are encoded as is_xref</p> <p>Data are available under the terms of the <a href="http://creativecommons.org/publicdomain/zero/1.0/">Creative Commons Zero "No rights reserved" data waiver</a> (CC0 1.0 Public domain dedication).</p>
Data from: Gigapixel big data movies provide cost‐effective seascape scale direct measurements of open‐access coastal human use such as recreational fisheries
Collecting data on unlicensed open‐access coastal activities, such as some types of recreational fishing, has often relied on telephone interviews selected from landline directories. However, this approach is becoming obsolete due to changes in communication technology such as a switch to unlisted mobile phones. Other methods, such as boat ramp interviews, are often impractical due to high labor cost. We trialed an autonomous, ultra‐high‐resolution photosampling method as a cost effect solution for direct measurements of a recreational fishery. Our sequential photosampling was batched processed using a novel software application to produce "big data" time series movies from a spatial subset of the fishery, and we validated this with a regional bus‐route survey and interviews with participants at access points. We also compared labor costs between these two methods. Most trailer boat users were recreational fishers targeting tuna spp. Our camera system closely matched trends in temporal variation from the larger scale regional survey, but as the camera data were at much higher frequency, we could additionally describe strong, daily variability in effort. Peaks were normally associated with weekends, but consecutive weekend tuna fishing competitions led to an anomaly of high effort across the normal weekday lulls. By reducing field time and batch processing imagery, Monthly labor costs for the camera sampling were a quarter of the bus‐route survey; and individual camera samples cost 2.5% of bus route samples to obtain. Gigapixel panoramic camera observations of fishing were representative of the temporal variability of regional fishing effort and could be used to develop a cost‐efficient index. High‐frequency sampling had the added benefit of being more likely to detect abnormal patterns of use. Combinations of remote sensing and on‐site interviews may provide a solution to describing highly variable effort in recreational fisheries while also validating activity and catch.
Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.
Data From: The Future of OA: A large-scale analysis projecting Open Access publication and readership
<p>This is the raw data behind the publication on bioRxiv at https://doi.org/10.1101/795310: </p> <p><strong>Piwowar, Priem, Orr (2019) The Future of OA: A large-scale analysis projecting Open Access publication and readership. bioRxiv: <a href="https://doi.org/10.1101/795310">https://doi.org/10.1101/795310</a></strong></p> <p>The jupyter notebook that produces the manuscript using the data here is available at: <a href="https://github.com/Impactstory/future-oa">https://github.com/Impactstory/future-oa</a></p> <p> </p> <p>Summary:</p> <p>Understanding the growth of open access (OA) is important for deciding funder policy, subscription allocation, and infrastructure planning.</p> <p>This study analyses the number of papers available as OA over time. The models includes both OA embargo data and the relative growth rates of different OA types over time, based on the OA status of 70 million journal articles published between 1950 and 2019.</p> <p>The study also looks at article usage data, analyzing the proportion of views to OA articles vs views to articles which are closed access. Signal processing techniques are used to model how these viewership patterns change over time. Viewership data is based on 2.8 million uses of the Unpaywall browser extension in July 2019.</p> <p>We found that Green, Gold, and Hybrid papers receive more views than their Closed or Bronze counterparts, particularly Green papers made available within a year of publication. We also found that the proportion of Green, Gold, and Hybrid articles is growing most quickly.</p> <p>In 2019:</p> <ul> <li> <p>31% of all journal articles are available as OA</p> </li> <li> <p>52% of article views are to OA articles</p> </li> </ul> <p>Given existing trends, we estimate that by 2025:</p> <ul> <li> <p>44% of all journal articles will be available as OA</p> </li> <li> <p>70% of article views will be to OA articles</p> </li> </ul> <p>The declining relevance of closed access articles is likely to change the landscape of scholarly communication in the years to come.</p>
Data from: Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne
Urine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we considered the mdx mice—a murine model of DMD—to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, a corticosteroid commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle control via liquid chromatography tandem mass spectrometry. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a metabolite with m/z = 357 and creatine, which were also reported in a previous human study looking at serum. Novel observations in this study included peaks identified as biliverdin and hypusine. These four metabolites were significantly higher at baseline in the urine of mdx mice compared to wild-type, and significantly changed their levels over time after baseline. Creatine and biliverdin levels were also different between treated and control groups, but for creatine this may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD or prednisolone treatment.
Figure 2 from: Kress W, Knapp S, Stoev P, Penev L (2012) On the front line of modern data-management and Open Access publishing: Two years of PhytoKeys – the fastest growing journal in plant systematics. PhytoKeys 19: 1-8. https://doi.org/10.3897/phytokeys.19.4501
Figure 2 - Taxonomic distribution by family of the published nomenclatural novelties in PhytoKeys.
Wu et al. Polysulfamide paper data - open access
<p>Data used in the main manuscript of "Investigating hydrogen bond-induced self-assembly of polysulfamides using molecular simulations and experiments" by Wu et al., published on Macromolecules in 2023</p>
Overdose Recovery and Care Access (ORCA) Qualitative Stakeholder Interviews and County-level Data
ClinicalTrials.gov study NCT06768814. IPD Sharing: NO. Countries: 1. Publications: 0.
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.