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934 results for “Amino acids”
Figure 2 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats
Figure 2. Graphical representation of necrosis percentage evolution obtained by photographic analysis in the burn interspace, two and seven days after injury in G1-Control, G2-Dip and G3-FreeAA. In the G3-FreeAA there was a significant reduction of necrosis between two and seven days *(P<0.05).
Figure 1 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats
Figure 1. Rat comb burn model: (A) Comb metal plate; (B) Comb burn injury, with four rectangular full-thickness burn areas separated by three unburned interspaces (stasis zone); (C) rectangular burned full thickness areas just after the injury; (D) animal from treated group 7 days after injury showing interspaces (stasis zone) without necrosis.
Figure 3 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 3: Chemotaxis (percent attracted) and mortality (percent of attracted worms dead) in the groups supplemented with L-phenylalanine or L-tryptophan and the control without amino acids. The error bars indicate standard deviation. The statistical differences were analyzed using one-way ANOVA, *P <0.05, **P <0.01.
Figure 2 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 2: GC-MS total ion chromatography of different samples. A: L-phenylalanine alone, strain 1.202 alone and strain cultured on water agar plus L-phenylalanine, benzaldehyde was increased and 1-Octen-3-ol was newly produced from strain 1.2052 cultures added L-phenylalanine; B: strain 1.202 alone, L-tyrosine alone and strain cultured on water agar plus L-tyrosine, benzaldehyde was decreased and 1-Octen-3-ol and indole were newly produced were produced from strain 1.2052 cultures added L-tyrosine.
Figure 1 in Chemotaxis of Caenorhabditis elegans Toward Volatile Organic Compounds from Stropharia rugosoannulata Induced by Amino Acids
Figure 1: Chemotaxis (percent attracted) of Caenorhabditis elegans toward Stropharia rugosoannulata stain 1.2052 cultured on water agar supplemented with amino acids. Controls are phenylalanine or tyrosine alone and strain 1.2052 alone. The error bars indicate standard deviation. The statistical differences were analyzed using one-way ANOVA, *P<0.05, **P<0.01.
Source Data for Supplementary Information of "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo"
<p>The attached excel file contains the source data for LC-MS traces shown in the Supplementary Information of the paper "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo." Each graph is contained in a tab and labeled with the Supplementary Figure number and panel with which it is associated.</p>
Figure 3 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 3. The incorporation of the amino acid L-lysine in C –C5 piperidine amide (4,5-dihydropiperine, 2) and two C -C 6 6 3 dihydropyridinone amides (trans-piplartine, 7 and cis-piplartine, 8).
Figure 2 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 2. HPLC analysis of the enzymatic reactions (L-phenylalanine + enzymatic extract of P. tuberculatum leaves). Chromatogram A shows the formation of the cinnamic acid product after incubation of the amino acid L-phenylalanine with the enzymatic extract. Chromatogram B show the the blank for comparison (L-phenylalanine + enzymatic extract of P. tuberculatum leaves, previously treated with 6M hydrochloric acid for enzyme inactivation). Chromatogram C shows the retention time of the phenylpropanoid cinnamic acid (standard). In addition to the amino acidL-phenylalanine, L-tyrosine was also used as a possible precursor to phenylpropanoids, but no conversion to p-coumaric acid was observed.The same results were observed for P. arboreum.
Figure 1 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 1. Piperine (1), 4,5-dihydropiperine (2), fagaramide (4), piperlonguminine (5), 4,5-dihydropiperlonguminine (6), trans-piplartine (7), cis-piplartine (8), and dihydropiplartine (9) are piperamides biosynthesized by P. tuberculatum; 4,5-dihydropiperiline (3) is biosynthesized by P. arboreum.
Assessing amino acid solubility of black soldier fly larvae meal in Atlantic salmon (Salmo salar) in vivo and in vitro
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Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
<p>Supplementary Material accompanying the manuscript titled "Anchored phylogenomics unravels the evolution of spider flies (Acroceridae) and reveals discordance between nucleotides and amino acids", including Supplementary Figures, Tables and Datasets.</p>
Structure and Stability of [4Fe-4S]-Maquettes with Non-coded Amino Acids
<p>The dataset provides supporting information to a hypothesis of coded Cys being thermodynamically superior to non-coded homoCys and thioGly analogues. The results were first presented at the 30/80 Chemobrionics 2019 meeting in Granada, Spain (www.chemobrionics.eu) and the corresponding publication appears in the thematic issue Frontiers Interface RSC journal.</p> <p>The data set organized accordingly to the published figures and tables.<br> Folders starting with numbers correspond to figures in the paper. The force field key files are to be used in combination of the amber99sb.prm force field, as provided by the Tinker 8.7 (dasher.wustl.edu/tinker/).</p> <p>The full secondary structure analysis was carried out using our in-house code (10.5281/zenodo.1442864).</p> <p>The folder 'trajectories' contains the peptides without the waterbath, while the 'waterbath' folder has the NPT equilibrated 6 nm waterbath in truncated octahedron geometry.</p> <p>The files starting with thermodynamics in the top folder has the numerical results used for calculating the cluster stability and ligand exchange reaction energetics.</p> <p>The folders 'reference cubane' and 'maquette with short peptides' contains the spin-polarized, ferro and antiferro-magnetically coupled electronic structure for all [4Fe-4S] cluster complexes.</p> <p>The key for the file extensions is as follows:</p> <p>FCHK: formatted Gaussian16 checkpoint file with spin polarized wave function<br> KEY: Tinker control keyword file<br> LOG: output file generated by a computer code<br> LST: clear text file with the content of a compressed tar archive<br> MSV: Discovery Studio Viewer Pro 5.0 binary file<br> MD5: file checksum according to MD5 protocol<br> ODS: Open Office electronic spreadsheet file<br> PDW: PsiPlot data file<br> PDB: Protein Databank Files<br> PGW: PsiPlot graphics file<br> PRM: Tinker force field parameter file<br> TGZ: compressed tar archive<br> TXT: clear text file or raw data set<br> TXYZ: Tinker XYZ file with atomic, positions, atom types, and connectivity <br> XYZ: Xmol file with atomic positions in Cartesian coordinates<br> </p>
Figure 1 in DNA damage, oxidative stress, decreased viability and motility in common carp (Cyprinuscarpio L.) spermatozoa induced by tryptophan, phenylalanine and cysteine amino acids during short-term storage
Figure 1. Effect of tryptophan (T), phenylalanine (P), cysteine (C) at concentrations of 1, 5, 25, and 50 mM on DNA fragmentation of common carp (Cyprinuscarpio L.) spermatozoa at 6 (a), 24 (b), and 48 (c) h.
Training data for "PepINVENT: Generative peptide design beyond the natural amino acids"
<p>The zipped file contains the training and the validation data used to train the PepINVENT model.</p>
Data to: Sulfur Amino Acid Status Controls Selenium Methylation in Pseudomonas tolaasii...
<p>data to: Sulfur Amino Acid Status Controls Selenium Methylation in Pseudomonas tolaasii: Identification of a Novel Metabolite from Promiscuous Enzyme Reactions</p> <p>Appl Environ Microbiol 2021 May 26;87(12):e0010421.</p> <p>doi: 10.1128/AEM.00104-21. Epub 2021 May 26.</p> <p> </p>
Code and Data for "Multiple re-reads of single proteins at single-amino-acid resolution using nanopores"
<p>The primary structures containing data and analysis products are peptidereads_fig2.mat (for figure 2) and peptiderereads_fig3.mat (for figure 3). The main analysis scripts for these data structures are callvariants_fig2.m and reread_analysis_fig3.m respectively. Data for figures S6 (S6_reread_data.dat) and S8 (S8_hetero_data.dat), and the analysis script used to produce figure S6 (S6_reread_analysis.m) are also included. Other files are dependencies of these main scripts.</p> <p> </p> <p>The fields in peptidereads_fig2 are as follows:</p> <p> </p> <p> </p> <p><strong>folder, eventnum, reducedStart, reducedEnd, suspicious, hasreread:</strong> notes for internal use</p> <p><strong>variant:</strong> the true identity of the single-amino-acid substitution variant</p> <p><strong>data: </strong>the ion current data for each read downsampled to 5 kHz.</p> <p><strong>omit: </strong>whether the read was omitted from analysis due to length</p> <p><strong>relativeDNAend</strong>: the index in the data where the DNA portion of the read ends.</p> <p><strong>relativeLinkerEnd:</strong> the index in the data where the linker portion of the read ends.</p> <p><strong>DNAlevels, Peplevels, Alllevels:</strong> extracted ion current levels for the DNA region, the peptide region, and everything.</p> <p><strong>cal: </strong>the multiplicative and additive constants applied to calibrate the read</p> <p><strong>caldata: </strong>the data with calibration constants applied</p> <p><strong>cons0D, cons0W, cons0G, cons0DNA: </strong>initial guesses for consensuses based on hand curation of data.</p> <p><strong>pepDcons0, pepWcons0, pepGcons0:</strong> the portion of the handmade consensus with the variant levels.</p> <p><strong>pepDcons, pepWcons, pepGcons:</strong> the portion of the iterated consensus with the variant levels.</p> <p><strong>inhandconsensus: </strong>whether the read was used in generation of the inital guess consensuses.</p> <p><strong>inconsensus</strong>: whether the read was used in generation of either the initial guess or iterated consensuses.</p> <p><strong>confidence:</strong> the relative likelihood of each variant assigned to the read</p> <p><strong>incalls:</strong> whether the data was used in variant calling (i.e., not used in consensus generation)</p> <p><strong>params</strong>: the analysis parameters used</p> <p> </p>
Micractinium rhizosphaerae NFX-FRZ genome annotation, fasta file, amino acid
<p>Micractinium rhizosphaerae NFX-FRZ annotation. FASTA file, amino acid.</p>
UniProt Human Proteome Benchmarking data for "aaHash: recursive amino acid hashing"
<p>aaHash is a rolling hash algorithm tailed for amino acids. Here, we provide the human proteome benchmarking data used in the aaHash paper "aaHash: recursive amino acid sequence hashing".</p>
Microbiome, mixotrophic algae, zooplankton, and fish amino acid and phospholipid fatty acid content in terrestrial and plastic carbon treatments
<p>Data includes amino acid (µg AA mg DW<sup>-1</sup>) and phospholipid fatty acid content (µg FA mg DW<sup>-1</sup>) of the microbiome, mixotrophic algae, zooplankton, and fish<em> </em>from the four-trophic level experiment. The experiment included control (no addition), 13.5% <sup>13</sup>C-labelled beech leaves (<em>Fagus sylvatica</em>), 97% <sup>13</sup>C-labelled lignin-hemicellulose extracted from wheat (<em>Triticum aestivum</em>, ~80% lignin, 13% hemicellulose), and 99% <sup>13</sup>C-labelled polystyrene (microplastic). Incubation time in humic lake water was 14 days in the control, leaf, and lignin experiment but 56 days for polystyrene, which after mixotrophic algae (<em>Cryptomonas </em>sp.) was introduced to the bottles. In the next step, herbivorous zooplankton (<em>Daphnia magna</em>) consumed microbes, mixotrophic algae, and particles for five days which after they were used as the diet to zebrafish (<em>Danio rerio</em>) during a five-day experiment.</p>
Data for: Genetic control of grain amino acid composition in a UK soft wheat mapping population
<p>Wheat is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain-free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed the identification of QTL controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following the identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programmes.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.