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355
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ShareScore release 0.9.0
Dataset results
355 results for “data extraction”
Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
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Data from: Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
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Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances
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Code for: <em>Triolena</em> anisophylly data extraction
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Data from: Deadwood structural properties may influence aye-aye (Daubentonia madagascariensis) extractive foraging behavior
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Data from: Extracting coherent tree-ring climatic signals across spatial scales from extensive forest inventory data
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Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods
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Data from: Increase in extraction of I-123 iomazenil in patients with chronic cerebral ischemia
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Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
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Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
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Data from: Geometric morphometric character suites as phylogenetic data: extracting phylogenetic signal from gastropod shells
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Data from: Can differential nutrient extraction explain property variations in a predatory trap?
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Data from: Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae
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Data from: Extractable soil lead (Pb) levels associated with increased soil carbon content in Mid-Atlantic turfgrass soils
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Detrended SSH data set used for Rossby Wave Analysis, extraction at 39N from ORCA12.L46-MJM189 DRAKKAR simulation
<p>This data set corresponds to the detrended Sea Surface Heigh (SSH) simulated by the NEMO ocean circulation model, under the ORCA12.L46-MJM189 configuration, developped in the frame of the DRAKKAR project. This particular data set is an interpolation from the native numerical grid, covering the latitude 39N in the North Altantic ocean, for the period 1970 to 2015. The data are concatenated in a single file with 5-days average of SSH. This subset was used in Watelet et al. (2020) submitted paper, dealing with Rossby waves analysis.</p>
Data from: Extracting phylogenetic signal from phylogenomic data: higher-level relationships of the nightbirds (Strisores)
A well-resolved phylogeny would facilitate study of adaptation to nocturnality in the avian superorder Strisores, a group that includes both nocturnal and diurnal lineages. Based on previous estimates, it could be hypothesized that there were multiple independent origins of nocturnality in this group. In order to refine the Strisores phylogeny, we generated genome-scale datasets of 2,289 – 4,243 ultra-conserved elements for 23 taxa representing all major living lineages in the group. Among the considerations for using genome-scale, molecular sequence data in phylogenomic analysis are issues related to GC content, GC variance and their effects on model selection. In this study, we employed a variety of analytical techniques to empirically investigate those issues in our data, as well as biases and errors resulting from alignment trimming, taxon selection and matrix completeness. Extensive analyses revealed conflict within the data, especially in regard to variation in GC content, that would not have been detected with more cursory study. Our results indicate that readily available models of molecular evolution are insufficient to encapsulate all phenomena present in genome-scale matrices, and that this problem may be at the root of many current issues in phylogenomic analysis. The analytical methods employed in this study are relevant to phylogenomic analysis of any large, heterogeneous matrix. In conclusion, we present a strongly supported estimate of the Strisores tree and discuss potential evolutionary pathways of nocturnality in this clade.
Data from: Validation of a simple extraction procedure for bisphenol A identification from human plasma
The general population is exposed to bisphenol A (BPA) orally, parenterally, transdermally, and environmentally as a result of the use of BPA in food packaging, plastics, and personal care products. The majority of the population nowadays (91–99%) has detectable levels of BPA inside their body. In this study, we successfully performed an inexpensive, rapid, and simple protein precipitation procedure for extraction of BPA from human plasma, followed by analysis by LC-MS/MS. This method was specifically developed for handling large numbers of samples with minimum cost and volume of sample. The developed method was accurate, precise, and reproducible for quantification of BPA from human plasma samples in the concentration range of 10–2000 ng/mL. The method was performed on samples from 150 healthy volunteers who were enrolled in the study. The mean of observed BPA level was 2.22 ± 9.91 ng/mL. Higher BPA levels were observed for females compare to that of males (p-value = 0.002), the BPA levels were higher in participants 33 years of age and older compared to those less than 33 years of age (p-value = 0.000), then the BPA levels higher in subjects with tap water as source of drinking (p-value = 0.005). This method may be valuable for general risk assessment of BPA for a large and varied population because of its efficiency and economical aspects.
Work Data Extraction and Recommendations
<p>Work Data Extraction and Recommendations</p>
Extended Cookbook Data Extraction and Recommendations
<p>Extended Cookbook Data Extraction and Recommendations</p>
Data from: Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish
Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2–0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.
ScienceDex guides
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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.