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.
57
datasets available to search
ShareScore release 0.9.0
Dataset results
57 results for “reagents”
Denaturing and dNTPs reagents improve SARS-CoV-2 detection via single and multiplex RT-qPCR
<p>The datas correspond to article entitled: "Denaturing and dNTPs reagents improve SARS-CoV-2 detection via single and multiplex RT-qPCR". </p> <p>The file entitle GISAID have the fasta formats for 107259 genomes from the SARS-CoV-2 GISAID database from January to December 2020. Three documents in plane tex correspond:<br> sequences.fasta contain the original data.<br> sequences_clean.fasta. Corresponds to genomes sequences without nucleotides undeterminateds indicates with "N" in previous document.<br> alignment_clean.fasta. Contain the genomes sequences cleaned alingment. </p> <p>The file entitle GenBank have the data set from 19317 genomes from the SARS-CoV-2 GenBank database from January to October 2020 and the documets have the prrevious order.</p>
Quantifying reagent spreading by cross borehole electrical tomography to assess performance of groundwater remediation
<p>This repository contains data related to the articleof the same name, published at Water Resources Research in 2022.</p> <p>inversion_inputs folder = all cross-borehole ERT/IP data formatted for the software AarhusInv</p> <p>inversion_results folder = output files from AarhusInv that can be used for plotting and further data analysis, for each inversion</p> <p>2x32_Z.xml = spread file for the ABEM Terrameter LS2 when two boreholes with 32 electrodes each are connected</p> <p>hvede_2xbsb.txt = quadrupole series for a given pair of boreholes, including the two single-borehole and two types of cross-borehole configurations. The electrodes order is A-B-M-N. Electrodes 1-32 are in borehole 1, while electrodes 33-64 are in borehole 2.</p> <p>hvede_2xbsb.xml = protocol file for the ABEM Terrameter LS2, that can be used in combination with the spread file 2x32_Z.xml.</p> <p>The paper abstract is given below.</p> <p>In-situ remediation of contaminated groundwater often relies on the installation of a treatment zone degrading the contamination. Zero-valent-iron (ZVI) is a type of reagent used for this purpose. Adequate delivery of ZVI in the whole target volume is particularly challenging and requires monitoring with high spatial resolution. We present a monitoring tool for imaging the dynamic spreading of ZVI and its associated ionic cloud, using cross-borehole time-lapse electrical resistivity tomography (ERT). This tool works in urban areas and is particularly suitable for achieving the required spatial resolution at the scale of the target volume. Groundwater and sediment samples show a consistent spatial and temporal distribution of the remediation cloud with cross-borehole ERT. Yet, the 2D anomalies observed with cross-borehole ERT provide a more spatially complete and rapid image of the remediation cloud distribution than if based solely on monitoring screens. At the study site, ZVI injection leads to uneven spreading, clearly documented by cross-borehole ERT monitoring. The benefit of hydraulic conductivity (K) mapping by cross-borehole induced polarization (IP) to understand unexpected injection paths (upstream leakage, spreading in preferred pathways) is investigated. A 2D, IP-based, continuous and coherent K-distribution is obtained that compares well with estimations by grain size analyses from the treatment zone. However, the IP-based K-field fails at predicting injection paths, suggesting the creation of pathways during the high-pressure injection of ZVI. Cross-borehole time-lapse ERT is the most promising geophysical tool for performance assessment of in situ remediation involving reagents with conductivity contrast.</p>
Squeegee: de novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes, simulation dataset 0.25% spike-in contaminant sequences
<p>Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic "bread crumbs” across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision.</p> <p> </p> <p>Simulation Dataset 0.25% contaminant spike-in.</p>
Squeegee: de novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes, simulation dataset 1% spike-in contaminant sequences
<p>Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic "bread crumbs” across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision.</p> <p> </p> <p>Simulation Dataset 1% contaminant spike-in.</p>
Electrodialysis with bipolar membranes for reagents recovery from dairy wastewater
<p>Poster presented in IEX24 regarding reagents recovery from dairy wastewater by using electrodialysis with bipolar membranes</p>
Erroneous Reagent Checking (ERC) benchmark
<p>The <strong>Erroneous Reagent Checking (ERC) benchmark</strong> assesses the accuracy of fact-checkers screening biomedical publications for dubious mentions of nucleotide sequence reagents. It comes with a test collection comprised of 1,679 nucleotide sequence reagents that were curated by biomedical experts.</p>
Room temperature iron-photopromoted arene C–H alkenylation without Grignard reagents
<p>Iron is inexpensive, non-toxic, and the most abundant transition metal in the earth's crust, rendering iron-catalysed C–H activations attractive yet particularly challenging. Despite major advances, iron-catalysed C–H activations have been linked to high reaction temperatures or the use of reactive Grignard reagents. Here, we present iron-catalysed ketimine C–H activations at ambient reaction temperature with the help of blue light in the absence of additives, utilising easily accessible <i>cis</i>-[Fe(H)2(dppe)2] (dppe = 1,2-bis(diphenylphosphino)ethane) as a single component precatalyst. Mild reaction conditions, high atom economy, and the lack of Grignard reagents are distinguishing features of the iron-catalysed C–H alkenylation manifold. Detailed mechanistic investigations by deuterium labelling, isolation of organometallic intermediates, and in operando LED-NMR spectroscopy revealed the role of the light and an oxidative addition to an iron(0) complex as the modus operandi for the C–H activation</p>
A risk-reward examination of sample multiplexing reagents for Single Cell RNA-Seq
<div> <h2>A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq</h2> <br> <div>The publication is available open access at https://doi.org/10.1016/j.ygeno.2024.110793</div> </div> <p>Be sure to check the md5 checksum: checklist.chk</p>
i-Pr2NMgCl·LiCl Enables the Synthesis of Ketones by Direct Addition of Grignard Reagents to Carboxylate Anions - NMR and HRMS data
<p>Primary raw data for the article published in Organic Letters DOI: 10.1021/acs.orglett.9b02899</p>
Experiment and analysis data of Study on the Effect of Pore-Clogging Caused by Fenton's Reagent on the Hydraulic Conductivity Using Time-lapsed Hydraulic Tomography
<p>The Microsoft Office Excel data file ('HT data.xlsx') contains two sheets: the first sheet includes the raw data from the first and second HT experiments, labeled as '1st' and '2nd' respectively; the second sheet contains their processed data.</p> <p>The compressed file ('Models.rar') includes all the models, such as the forward and inverse models. Each model contains its own input files and an executable file.</p>
Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation
<p>Data underlying the figures in the publication “Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation”, published in <em>ChemBioChem</em>, <strong>2020</strong>, 21, 3515– 3520.</p> <p><a href="https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000557">https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202000557</a></p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Zip file containing the MNOVA files for the <sup>1</sup>H and <sup>13</sup>C NMR spectra of compounds <strong>1-18</strong> in <em>Scheme 1</em>.</p>
Raw data for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents "
<p>Raw computational, NMR, IR and MS data for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents " published in Chemical Science, DOI: </p> <p><a href="https://doi.org/10.1039/D2SC04344K">https://doi.org/10.1039/D2SC04344K</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Raw data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization"
<p>Raw NMR, HPLC and MS data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization" published in Angewandte Chemie, DOI: </p> <p><a href="https://doi.org/10.1002/anie.202306036">https://doi.org/10.1002/anie.202306036</a> </p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions
<p>Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.</p>
The cell wall changes as a result of the disturbed presence of AGPs by Yariv reagent addition.
<p>The deposited data were collected as a part of the studies entitled ‘How does the structure of the cell wall change as a result of the disturbed presence of AGPs by Yariv reagent addition?’</p> <p>The research is the result of cooperation between institutions: Institute of Agrophysics, Polish Academy of Sciences (Poland), and Department of Chemistry, Brown University (USA). The use of advanced microscopic techniques (immunolabeling method), methods of molecular biology (Western blotting, ELISA) allows for expanding knowledge in the field of plant cell physiology and biochemistry. </p> <p> </p> <p>The attached files have been compressed to *.zip format. The dataset consists of the following files:</p> <p>A_1_CLSM imaging</p> <p>A_2_ELISA</p> <p>A_3_Western blotting.</p>
FIGURE. Roussoella pseudohysterioides (GMB0009). a–d. Ascostromata developing on bamboo culm. e, f. Vertical sections of ascostromata. g–j. Asci containing eight ascospores. k. Fragment of ascostromata in KOH without stromatal pigments. l–m. Ascus apex in Melzer's reagent. n–r. Dark brown ascospores. Scale bars: j–r = 10 μm. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Roussoella pseudohysterioides (GMB0009). a–d. Ascostromata developing on bamboo culm. e, f. Vertical sections of ascostromata. g–j. Asci containing eight ascospores. k. Fragment of ascostromata in KOH without stromatal pigments. l–m. Ascus apex in Melzer's reagent. n–r. Dark brown ascospores. Scale bars: j–r = 10 μm.
Stereodynamical control of the H+HD→H2+D reaction through HD reagent alignment
<p><span>Prealigning nonpolar reacting molecules leads to large stereodynamical effects because of their weak steering interaction en route to the reaction barrier. However, experimental limitations in preparing aligned molecules efficiently have hindered the investigation of steric effects in bimolecular reactions involving hydrogen. Here we report a high-resolution crossed-beam study of the reaction H+HD(<em>ν</em>=1, <em>j</em>=2)→H<sub>2</sub>(<em>ν</em>', <em>j'</em>)+D at collision energies of 0.50, 1.20, and 2.07 electron volts, in which the vibrationally excited hydrogen deuteride(HD) molecules were prepared in two collision configurations, with their bond, preferentially aligned parallel and perpendicular to the relative velocity of collision partners. Notable stereodynamical effects in differential cross-sections were observed. Quantum dynamics calculations revealed that strong constructive interference in the perpendicular configuration plays an important role in the stereodynamical effects observed.</span></p>
COG-REAGENT: COGnitive tRaining in patiEnts With Amnestic Mild coGnitive impairmENT
ClinicalTrials.gov study NCT04063956. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Phase I Clinical Trial Immunizing Healthy Adults With the NMRC-M3V-Ad-PfCA Vaccine to Generate Biologic Reagents
ClinicalTrials.gov study NCT01843491. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Stereodynamical control of the H+HD→H2+D reaction through HD reagent alignment
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.