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.
92
datasets available to search
ShareScore release 0.9.0
Dataset results
92 results for “18S rRNA”
Fig. 3 in Usefulness of PCR-RFLP of 18S rRNA gene for rapid post-mortem diagnostics of highly pathogenic Eimeria spp. (Apicomplexa: Eimeriidae) of European bison, Bison bonasus L. with histopathological correlation
Fig. 3. The virtual double digestion of the 18S rRNA gene of eimerians infecting the large intestine of the European bison with the restriction enzymes Mval (BstNI) recognising CC∧WGG, and KpnI recognising GGTAC∧C, simulated with SnapGene version 5.0.6 (GSL Biotech LLC); M: GeneRuler 50 bp DNA Ladder (Thermo Fisher Scientific). (A) A three-band pattern for E. bovis (20 bp, 210 bp, 343 bp). (B) A four-band pattern for E, zuernii (20 bp, 100 bp, 210 bp, 242 bp). (C) A two-band pattern for E. alabamensis (212 bp, 362 bp).
Fig. 1 in Usefulness of PCR-RFLP of 18S rRNA gene for rapid post-mortem diagnostics of highly pathogenic Eimeria spp. (Apicomplexa: Eimeriidae) of European bison, Bison bonasus L. with histopathological correlation
Fig. 1. Histopathological lesions associated with endogenous stages of Eimeria spp. in sections of the ileum and colon of European bison (H-E staining). (A) Shortening and blunting of the intestinal villi of the ileum with diffuse infiltration of mononuclear inflammatory cells within the lamina propria, edematous stroma, dilated crypt containing necrotic debris (arrow), and atrophy of submucosal lymphoid follicles (× 20 magnification). (B) Schizonts and degenerating merozoites in the crypt lumen of the colon (arrows); immature macrogamont with a central nucleus (arrowhead) (× 1000 magnification). (C) Immature microgamonts in the epithelial cells of the colon crypt (arrows) (× 400 magnification). (D) Mature microgamont in the epithelial cells of the colon crypt (arrow) (× 1000 magnification). (E) Gametogonic stages of Eimeria development in the epithelial cells of the colon. Microgamont with peripheral microgames (arrowhead), (a) nearly mature microgamonts, (b) macrogamont with eosinophilic wall-forming bodies, (c) early oocyst (× 400 magnification). (F) Mature macrogamont in the epithelial cells of the cecum (arrow) (× 1000 magnification).
Fig. 2 in Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing
Fig. 2. Relative abundance of all parasite genera detected from fecal samples of wild carnivores in Korea. The relative abundance of each parasite is defined as the ratio of the number of sequence reads assigned to that parasite to the total number of sequence reads assigned to all target parasites.
Fig. 1 in Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing
Fig. 1. Diversity of fecal parasitomes of wild carnivores in Korea. The results shown are based on the diversity of zero-radius operational taxonomic units (ZOTUs) that were taxonomically assigned to parasites. (a) Comparison of richness and diversity of parasite ZOTUs between host animals estimated by the Chao1 estimator and Shannon index, respectively. (b) Non-metric multidimensional scaling (NMDS) plots showing the structure and membership of parasite ZOTUs represented by the Bray–Curtis dissimilarity and Jaccard index, respectively. In the panel (a), one asterisk (*) and two asterisks (**) represent p <0.05 and p <0.01, respectively, by the post hoc Wilcoxon rank-sum test. The abbreviation "ns" represents no statistical difference.
Figure 4. 18S rRNA strict consensus tree from 12 in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules
Figure 4. 18S rRNA strict consensus tree from 12 most parsimonious trees (3228 steps, CI = 0.4786, RC = 0.3076). Above branches are 'bootstrap proportion | decay index', below are 'Bayesian posterior probability | ML-puzzling proportion'. Arrows indicate the 'thraciid' (T) and 'lyonsiid' (L) lineages.
Figure 5 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 5. Summary cladogram representing the relationships of the anomalodesmatan family-level taxa inferred from the 18S rRNA data. Asterisks indicate lacking support for the monophyly of the taxon.
Figure 3 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 3. Maximum-likelihood tree under an HKY85+I+G model (–logL = 25513.945, s/v ratio = 1382, pinvar = 0.189, gamma = 0.463).
Figure 2 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 2. Strict consensus tree of 22 most parsimonious trees using all alignment positions of the 18S rRNA data set. Bootstrap values (above branches) refer to 1000 replications, maximum-likelihood puzzling values (below branches; values lower than 30 not given) refer to 100 000 puzzling steps. A, subtree showing the position of Anomalodesmata among the Heterodonta. B, subtree of the Anomalodesmata. Pha., Pharidae; Ven., Veneridae. Asterisks mark species of the polyphyletic Myoida. Arrowheads indicate the anomalodesmatan nodes collapsing when 506 positions of uncertain alignment in the
Figure 1 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 1. Single most parsimonious tree resulting from the analysis of the entire morphological data set of Harper et al. (2000). Asterisks mark taxa not available for the present study. The Euciroidae as recognized by Poutiers & Bernard (1995) was not separated from the Verticordiidae.
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S rRNA concatenated dataset showing position of Laubierpholoe massiliana Zhadan sp. nov. within Sigalionidae Kinberg, 1856. Posterior probabilities and bootstrap values are shown for each medium supported node.
Modena E. coli (16S and 23S) and S. cerevisiae (18S and 25S) rRNA test dataset samples 1 to 5
<p>Samples 1 to 5 of the rRNA test dataset accompanying the article "<em>Nanopore based computational method for detecting a wide range of epigenetic/epitranscriptomic modifications".</em></p> <p>Each sample comprises seven subsamples with coverage depths ranging from 10 to 2000.</p> <p>If you have any questions about the content of this dataset, feel free to contact Siniša Biđin at sinisa@heuristika.hr.</p>
Modena E. coli (16S and 23S) and S. cerevisiae (18S and 25S) rRNA test dataset samples 6 to 10
<p>Samples 6 to 10 of the rRNA test dataset accompanying the article "<em>Nanopore based computational method for detecting a wide range of epigenetic/epitranscriptomic modifications".</em></p> <p>Each sample comprises seven subsamples with coverage depths ranging from 10 to 2000.</p> <p>If you have any questions about the content of this dataset, feel free to contact Siniša Biđin at sinisa@heuristika.hr.</p>
Example dataset for 18S rRNA microbial community analysis
<p>Original, trimmed (sequencing primers removed) and trimmed+subsampled reads for the Study Group lesson on Microbial Ecology.</p>
Modena test datasets: human 18S rRNA, curlcakes, oligos, oligos mixtures
<p>The human 18S rRNA, curlcakes, oligos and oligos mixtures test datasets accompanying the article "<em>Nanopore based computational method for detecting a wide range of epigenetic/epitranscriptomic modifications".</em></p> <ol> <li>Human 18S rRNA dataset contains a control sample and a native sample. Each sample comprises six subsamples with coverage depths ranging from 10 to 500.</li> <li> <p>Curlcake-M1 dataset contains a single sample. This sample comprises eight subsamples with coverage depths ranging from 10 to 1000. For each given coverage depth, a subsample contains four modified curlcakes, where each adenine (A) was replaced with m6A. Curlcake-UNM1 dataset contains a single sample. This sample comprises eight subsamples with coverage depths ranging from 10 to 1000. For each given coverage depth, a subsample contains four unmodified curlcakes. Curlcake-M2 dataset contains a single subsample with a coverage depth of 2000. This subsample contains four modified curlcakes, where each adenine (A) was replaced with m6A. Curlcake-UNM2 dataset contains a single subsample with a coverage depth of 2000. This subsample contains four unmodified curlcakes.</p> </li> <li> <p>Oligo-1, Oligo-2 and Oligo-3 contain three modified samples of the three Oligos variants, while Oligo-C contains three unmodified samples. Each sample comprises eight subsamples with coverage depths ranging from 10 to 2000.</p> </li> <li> <div>Oligo-mixtures dataset contains 10 samples. Each sample comprises subsamples with coverage depths ranging from 10 to 2000. Additionally, for each sample and coverage depth, there are three different mixtures. Each of these three mixtures has a ratio of modified to unmodified reads of either 25:75, 50:50, or 75:25.</div> </li> </ol> <p>If you have any questions about the content of this dataset, feel free to contact Siniša Biđin at sinisa@heuristika.hr.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data for: Visualization of the hidden food sources of bass (Micropterus salmoides), crucian carp (Carassius carassius), and minnow (Zacco platypus) using 18S rRNA V9 primers on urban Singal Reservoir in Korea
<p>Fish are the most important consumers in aquatic ecosystems, and the analysis of fish prey is very important for understanding their short-term feeding characteristics and the connectivity of food webs. In this study, DNA metabarcoding was used to identify the prey of the native fish species, <em>Zacco platypus</em> (the pale chub) and <em>Carassius carassius</em>, and an introduced species, <em>Micropterus salmoides</em>, in domestic lentic ecosystems. Prey community composition, selectivity index, prey diversity, and trophic level analyses were performed. The prey composition ratio analysis showed that in August 2020, 85.8% of <em>M. salmoides</em>' prey was fish from the orders Cypriniformes and Perciformes, and in July 2021, 100% of <em>M. salmoides</em>' prey was zooplankton from the orders Anomopoda and Calanoida. Zooplankton was the main prey of <em>Z. platypus</em> collected in August 2020 (69.5%) and <em>C. carassius</em> collected in July 2021 (88.9%). The selectivity index analysis showed that the preferred prey of M. salmoides was fish from the order Cypriniformes, the preferred prey of <em>Z. platypus</em> was phytoplankton from the division Bacillariophyta, and the preferred prey of <em>C. carassius</em> was zooplankton from the order Cladocera. For the prey width analysis, <em>C. carassius</em> had the highest BI index value (0.8), followed by <em>Z. platypus</em> (0.29), while <em>M. salmoides</em> had BI index values of 0.09, 0.19, and 0.001, indicating low prey width. These results provide fundamental data on the utility of DNA metabarcoding for dietary studies of major fish species in lentic ecosystems and for analyzing food web connectivity based on major prey items.</p>
18s rRNA sequence
<p>Our eukaryotic <a href="https://www.cd-genomics.com/microbioseq/eukaryotic-18s-rrna-sequencing.html">18S rRNA sequence</a> determines the specific 18S ribosomal RNA (rRNA) genes of eukaryotes and yeast using the next-generation sequencing (NGS) and long-read sequencing platforms. This service helps reveal the microbial community structure, the evolutionary relationship of eukaryotes, and the correlation between eukaryotes and the environment.</p><p> </p>
Data for: Visualization of the hidden food sources of bass (Micropterus salmoides), crucian carp (Carassius carassius), and minnow (Zacco platypus) using 18S rRNA V9 primers on urban Singal Reservoir in Korea
Open the record for dataset details and reuse information.
Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models
BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. RESULTS: Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. CONCLUSION: An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.
Data from: 18S rRNA metabarcoding diet analysis of the predatory fish community across seasonal changes in prey availability
Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n=367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited compositional changes in diet. Dietary overlap was slightly but significantly higher during the period of high prey abundance. There was little evidence for large changes in predator preference between the two periods. This study demonstrates the utility of molecular diet analysis in understanding predator-prey interactions in complex freshwater communities.
Fig. 2 in Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols
Fig. 2 Box-and-whisker plot of intraspecific and intrageneric (x-axis) genetic distances measured in uncorrected p-distances (y-axis). Thick black lines indicate median values, boxes represent upper and lower quartiles, whiskers indicate value ranges, circles represent outliers
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.