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.
126
datasets available to search
ShareScore release 0.9.0
Dataset results
126 results for “Extraction Method”
Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
<p>Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment. Collecting and identifying eDNA has gained popularity for monitoring and surveillance of aquatic invasive species. Invasive species management is most successful when an invasion is identified early while population size is likely to be low, highlighting the importance of eDNA detection sensitivity. Various factors influence DNA yield recovered from environmental samples. Environmental DNA storage and extraction methods, for example, can be adjusted to maximize DNA yield, thereby improving detectability. In this study, we compared the performance of two eDNA storage and extraction methods in detecting three common aquatic invasive species (<em>Bythotrephes longimanus</em>, <em>Dreissena polymorpha</em>, and <em>Faxonius rusticus</em>) across five natural ecosystems of Minnesota, United States. One method involved storing filters in 95% ethanol (EtOH) and extracting DNA using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany), whereas the other method used cetyl trimethylammonium bromide (CTAB) for storage and a phenol–chloroform–isoamyl (PCI) procedure for DNA extraction. We also investigated the effect of DNA extract volume (1 μL relative to 3 μL) in qPCR reactions on eDNA detections for the commercial kit method. The CTAB‐PCI method yielded significantly more positive detections, across all three species, compared to the EtOH‐Qiagen method. Moreover, we found that using 1 μL of DNA extract in qPCR reactions was equally effective as using 3 μL. To improve detections of aquatic invasive species, we recommend that researchers store eDNA sample filters in CTAB or a similar lysis buffer such as Longmire's solution and extract with PCI when feasible, but note that lower extract volumes might be used without negative effect when either increasing technical replicates or repurposing samples for the detection of multiple species.</p>
Data from: Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens
<p>The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, <em>Melitaea diamina</em>, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.</p>
A STP-HSI index method for urban built-up area extraction based on multi-source remote sensing data
<p>The changes of urban built-up areas can reflect the process of urbanization, and it can reflect the population, economy, and cultural development of the city. Therefore, accurate and timely extraction of urban built-up areas plays an important role in the dynamic management of the city. In the existing research, single-source remote sensing data is used to extract urban built-up areas, and there is a problem that the spectrum of urban areas and non-urban areas is easily confused. Multi-source remote sensing data, including luojia-1 remote sensing data, Landsat 8 OLI remote sensing data, etc., can make up for the spectrum confusing issues.</p> <p>We fuse the time series information of night light remote sensing data, neighborhood information and point of interest (POI) data in spatial dimension, and propose a built-up area extraction method that integrates night light time and space information and POI information.</p>
Dataset for "Surf-Net: A deep-learning-based method for extracting surface-wave dispersion curves"
<p>dataset for the article "Surf-Net: A deep-learning-based method for extracting surface-wave dispersion curves"<br> corrLSynV8.h5: the generated synthetic waveform<br> dispersion.tar : the dispersion curves set for the generated synthetic waveform; the dispersion curves extracted in Northeast China; the dispersion curves extracted in Southeast China</p>
Results of integrating asynchronous data provenance methods, metadata extraction, and similarity detection into a standards-based RDMS
<p>Related to the thesis: "Asynchronous Tracking and Description of Research Data Changes in Distributed Systems with Interoperable Metadata"</p>
Data for: A new threshold selection method for species distribution models with presence-only data: extracting the mutation point of the P/E curve by threshold regression
Open the record for dataset details and reuse information.
Data from: Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens
Open the record for dataset details and reuse information.
A STP-HSI index method for urban built-up area extraction based on multi-source remote sensing data
Open the record for dataset details and reuse information.
Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
Open the record for dataset details and reuse information.
FucoSan: Extraction of fucoidans from different brown algae species using different methods and their chemical and biological characterization
<p>This is a dataset extracted from the database of the Interreg project “FucoSan – Health from the sea” which includes information on the used algae species, the extraction of fucoidans as well as their chemical and pharmacological characterization.</p> <p>Macroalgae represent a vast source of renewable raw materials for research, development and application. An example of current high interest are fucoidans from brown algae. These fucose-containing sulfated polysaccharides exhibit a multitude of bioactivities offering attractive options for applications in medicine and cosmetics. The composition and chemical structure of fucoidans and thus their bioactivities may, however, largely vary depending on the algae species, extraction procedure and many other factors. Therefore, much research is still needed in the range from the algal source up to the targeted development of fucoidans optimized for respective applications. Since 2017, this is the topic of the Danish-German project Interreg project “FucoSan – health from the Sea” involving 11 partners with different expertise. Here, the current state of the fucoidan series produced and explored within the project is presented including information on the used algae species and batches, the extraction, purification and fractionation of the fucoidans as well as their chemical and pharmacological characterization. Based on their basic pharmacological activities, fucoidans are then selected and further tested in advanced experiments for specific applications in medicine and cosmetics.</p>
Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria
High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial communities' characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in term of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artifactual sequences and contaminations, as well as noticeable differences in bacterial communities' characteristics were observed between the extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbor different bacterial communities. Our benchmark hence suggests that cuticular microbiota of single insect individuals can be reliably retrieved provided that blank controls, appropriate data cleaning, and standardization of individual body size are considered in the experiment.
Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
Humic substances are break-down products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution, and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content, and remove humics, producing clean samples easily analyzed by mass spectrometry (MS). This method includes: 1) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; 2) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; 3) centrifugal stage-tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (~800¬–1000 yr) dark with humic content, generating colorless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics, and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
Figs. 14–15 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 14–15. Number of Coleoptera specimens obtained at predetermined time intervals in two trials to test ECOLI protocol. 14) Trial A, Coleoptera specimens obtained from Berleses and Winklers at the initial 24-hr interval, during the intermediate interval at 96 hrs, and at the terminal extraction interval of 216 hrs; 15) Trial B, Coleoptera specimens obtained from Berleses and Winklers at the initial 24-hr interval and the terminal extraction interval of 216 hrs following an intermediate resting period from 24–96 hrs.
Figs. 12–13 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 12–13. Accumulation of specimens of Curculionidae obtained from six litter samples across extraction intervals. 12) Berlese funnels; 13) Winkler funnels.
Figs. 8–9 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 8–9. Accumulation of specimens of "rare" Coleoptera species obtained from six litter samples across extraction intervals. 8) Berlese funnels; 9) Winkler funnels.
Figs. 6–7 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 6–7. Accumulation of Coleoptera species obtained from six litter samples across extraction intervals. 6) Berlese funnels; 7) Winkler funnels.
Figs. 10–11 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 10–11. Accumulation of specimens of Staphylinidae obtained from six litter samples across extraction intervals. 10) Berlese funnels; 11) Winkler funnels.
Figs. 2–3 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Figs. 2–3. Flow chart diagramming test of ECOLI protocol. 2) Trial A, sample continuously run with three extraction intervals at 24, 96, and 216 hrs; 3) Trial B, sample run with initial collection interval at 24 hrs, "resting" period from 24–96 hrs, and terminal extraction interval at 216 hrs.
Fig. 1 in "Berlese vs. Winkler": Comparison of Two Forest Litter Coleoptera Extraction Methods and the Ecoli (Extraction of Coleoptera in Litter) Protocol
Fig. 1. Map of the southern United States showing locations of litter sample field sites. Polk County, Arkansas; West Feliciana Parish, Louisiana; Winston County, Alabama; Cochise County, Arizona; Swain County, North Carolina; Hidalgo County, New Mexico; Sabine County, Texas.
Evaluation of different methods to extract DNA from serum seeded with methicillin-resistant Staphylococcus aureus
Open the record for dataset details and reuse information.
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.