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.
68
datasets available to search
ShareScore release 0.9.0
Dataset results
68 results for “environmental sequencing”
Mullus surmuletus environmental DNA intraspecific metabarcoding Next-Generation Sequencing data
<p>Four 250-liter aquariums were bleached clean one day prior to be used (filled with seawater; fish transfer) in Montpellier (France). Seawater collected by the French Research Institute for Exploitation of the Sea at Palavas-les-Flots (France) was first stored in a 1,000 L tank for two weeks, under UV treatment to avoid any contamination. The aquariums were then filled with 120 L of this water. Each aquarium had a closed-circuit water circulation and was equipped with an air bubbles exhauster in a tube that brought up the water on a neutral synthetic foam filter. The aquariums were thus oxygenated and the coarsest suspended matter was filtered out. The remaining seawater in the tank was used as a negative control (Aquarium 1). Nine to eleven fish were added to each of the four aquariums (Fig. 1). The aquarium water was sampled six hours after introducing the fish into the aquariums using an Athena peristaltic pump (SPYGEN, Le Bourget-du-Lac, France) with a nominal flow of 1.0 L/min to filter 30 L, and VigiDNA 0.22 μm crossflow filtration capsules (SPYGEN) with disposable sterile tubing. After filtration, 80 mL of CL1 conservation buffer (SPYGEN) was added before storing the samples at ambient temperature.</p> <p> </p> <p>We reanalyzed here two eDNA samples of 30 L replicate each, collected in the Mediterranean Sea, at Banyuls (France, coordinates: 42.41568, 3.17110) and Calvi (France, coordinates: 42.62964, 8.89161) published in a previous metabarcoding analysis and known to contain <em>M. surmuletus</em> sequences (detected with the metabarcode teleo 12S) (Boulanger <em>et al.</em> 2021). These two Mediterranean eDNA samples were amplified and sequenced using the primers developed for this study and then analyzed using the best-performing pipeline as determined by our evaluation. These two samples were used as proof of concept of the possibility to estimate within site variability in real conditions.</p> <p> </p> <p> </p> <p>DNA extraction and amplification from eDNA samples were performed by the company SPYGEN (Le Bourget du Lac, France) in separate, dedicated rooms following the protocol described by Polanco Fernández <em>et al.</em> (2020). The amplification was performed in a final volume of 25 μL including 1 U of AmpliTaq Gold DNA Polymerase (Applied Biosystems, Foster City, CA, USA), 10 mM of Tris-HCl, 50 mM of KCl, 2.5 mM of MgCl2, 0.2 mM of each dNTP, 0.2 μM of each primer, 0.2 μg/μL of bovine serum albumin (Roche Diagnostics, Basel, Switzerland) and 3 μL of DNA template. The PCR mixture was denatured at 95°C for 10 min, followed by 50 cycles of 30 s at 95°C, 30 s at 47°C and 1 min at 72°C and a final elongation step at 72°C for 7 min. The primers were 5’-labelled with an eight-nucleotide tag unique to each DNA sample, allowing each sequence to be assigned to the corresponding sample during the sequence analysis. Twelve replicate PCRs were run per sample. Two libraries were prepared using the MetaFast protocol (Fasteris 2020, <a href="https://www.fasteris.com/dna/">https://www.fasteris.com/dna/</a>) and the sequencing was performed by Fasteris (Geneva, Switzerland) on two separate runs on an Illumina MiSeq (2x250 bp) (Illumina, San Diego, CA, USA) and the Miseq Kit v3 (Illumina) following the manufacturer’s instructions. Two negative extraction controls and one negative PCR control (12 replicates of ultrapure water) were amplified and sequenced to monitor for possible contaminants (Polanco Fernández <em>et al.</em>, 2020).</p> <p> </p> <p> </p> <p> </p>
OTUs Table and fastq sequences from environmental DNA applied to trematode communities
<p>This OTUs table and fastq sequences underlie the main results of the study "Make visible the invisible: Optimized development of an environmental DNA metabarcoding tool for the characterization of trematode parasitic communities".</p> <p>In this study, our aim was to develop an optimized eDNA-based metabarcoding approach to detect trematodes and characterize their communities, most of which associated to aquatic environments. We thus assessed the ability of our eDNA-based metabarcoding approach to reconstruct trematode communities compared to a classical trematode monitoring method over four freshwater aquatic ecosystems. </p> <p>We focused on 4 natural sites from Occitanie Region (Southern France) that differ in terms of habitats, and in which the trematode communities were previously at least partially characterized. At each of these sites, we sampled the water-sediment interface from which the eDNA was extracted and sequenced with a MiSeq amplicons sequencing approach. <br> Over the four natural ecosystems screened in nature, 33 OTUs were generated from the eDNA-based approach, from which 11 trematode species were identified. In comparison, we identified five trematode species using the classical monitoring method, three of which were also detected by the eDNA-based approach.</p>
Supplementary material 2 from: Naro-Maciel E, Ingala MR, Werner IE, Reid BN, Fitzgerald AM (2022) COI amplicon sequence data of environmental DNA collected from the Bronx River Estuary, New York City. Metabarcoding and Metagenomics 6: e80139. https://doi.org/10.3897/mbmg.6.80139
Tables S1,S2, Figures S1–S3
Supplementary material 1 from: Naro-Maciel E, Ingala MR, Werner IE, Reid BN, Fitzgerald AM (2022) COI amplicon sequence data of environmental DNA collected from the Bronx River Estuary, New York City. Metabarcoding and Metagenomics 6: e80139. https://doi.org/10.3897/mbmg.6.80139
Supplementary Data Files 1, 2
Supplementary material 10 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Abundance of some common fish species obtained by the direct visual census
Supplementary material 2 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Primer, index and probe sequences used in the study
Supplementary material 1 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The numbers of sequence reads remaining (filtered) in data processing steps
Supplementary material 7 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Results of quantitative PCR for total fish eDNA, Japanese anchovy and Japanese jack mackerel
Supplementary material 3 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Descriptions of TaqMan probe specificity test and supplementary Table S1 and S2
Data from: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
Open the record for dataset details and reuse information.
Data from: Diversity measures in environmental sequences are highly dependent on alignment quality—data from ITS and new LSU primers targeting basidiomycetes
Open the record for dataset details and reuse information.
Data from: Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data
Open the record for dataset details and reuse information.
OTUs Table and fastq sequences from environmental DNA applied to trematode communities
Open the record for dataset details and reuse information.
Data from: Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA
Open the record for dataset details and reuse information.
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface Kirovograd region soil Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FXRalpha-/- testicular Transcriptomes with Environmental Exposure
GEO Series GSE119012. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
In situ tumor arrays reveal early environmental control of cancer immunity [Whole Exome Sequencing]
GEO Series GSE222540. Mus musculus. 11 samples. Type: Other.
RNA sequencing of whole Dorsal Root Ganglia (DRG) and laser captured large diameter DRG neurons upon Environmental Enrichment (EE) compared to Standard Housing (SH)
GEO Series GSE125793. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Data from: From environmental DNA sequences to ecological conclusions: how strong is the influence of methodological choices?
Aim: Environmental DNA (eDNA) is increasingly used for analysing and modelling all-inclusive biodiversity patterns. However, the reliability of eDNA-based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps, and identify the crucial ones to draw sound ecological conclusions. Location : Valloire, French Alps. Taxon: Vascular plants and Fungi. Methods: Using soil eDNA metabarcoding data for plants and fungi from twenty plots sampled along a 1000-m elevation gradient, we tested how the conclusions from three types of ecological analyses: (i) the spatial partitioning of diversity, (ii) the diversity-environment relationship, and (iii) the distance-decay relationship, are robust to data curation steps. Since eDNA metabarcoding data also comprise erroneous sequences with low frequencies, diversity estimates were further calculated using abundance-based Hill numbers, which penalize rare sequences through a scaling parameter, namely the order of diversity q (Richness with q=0, Shannon diversity with q~1, Simpson diversity with q=2). Results: We showed that results from different ecological analyses had varying degrees of sensitivity to data curation strategies and that the use of Shannon and Simpson diversities led to more reliable results. We demonstrated that MOTU clustering, removal of PCR errors and of cross-sample contaminations had major impacts on ecological analyses. Main conclusions: In the Era of Big Data, eDNA metabarcoding is going to be one of the major tools to describe, model and predict biodiversity in space and time. However, ignoring crucial data curation steps will impede the robustness of several ecological conclusions. Here, we propose a roadmap of crucial curation steps for different types of ecological analyses.
Data from: From environmental DNA sequences to ecological conclusions: how strong is the influence of methodological choices?
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.