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253
datasets available to search
ShareScore release 0.9.0
Dataset results
253 results for “amplicons”
Data from: Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
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Data from: Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.)
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Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
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Data from: Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing
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Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing
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Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons
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Coregonus spp. opsin amplicon sequence alignments
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Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)
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Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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NGS amplicon metagenomic 16S seq of soybean rhizosphere under contrasting nutrient-deficient and acidic-stress soils
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Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing
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Data from: The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia
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Data from: Within-host competition between Borrelia afzelii ospC strains in wild hosts as revealed by massively parallel amplicon sequencing
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Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences
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OTUreporter: from amplicon to report in a single command
<p>Full test dataset and output for OTUreporter amplicon pipeline.</p> <p>Contents:</p> <ul> <li><strong><em>full_dataset_out.tar</em></strong>: output of the OTUreporter analysis for the full test dataset. Most intermediate files from the mothur_out/ folder have been removed to reduce the size.</li> <li><strong><em>full_sample_dataset.tar</em></strong>: includes the fastq.gz files from all samples and controls of the full test dataset. Generated by the UNSW MICR2011 course in 2019.</li> <li><em><strong>sample_reports.tar.gz</strong></em>: final reports from the analysis of the full test dataset packaged separately for convenience.</li> </ul>
Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing
<p>Non-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. <span>The information lost when genotyping success is low may lead to decreased precision in animal population densities, which could misguide conservation and management actions.</span> <span>Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories.</span> Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using multiplexed amplicon sequencing optimized for degraded DNA. <span>We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (<i>Canis latrans</i>) using 26 SNPs. </span><a name="_Hlk33181599">Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies while remaining at a low cost of under $5 per PCR replicate (excluding labor). </a>The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.</p>
Amplicon sequencing of endolithic microbial communities of Joshua Tree National Park, California (USA)
<p>ITS and 16S amplicon sequencing data of ten rock samples, colonized by endolithic communities, collected at Joshua Tree National Park (May 2016). The Ribosomal Internal Transcribed Sequence 1 region (ITS1) and V4 region of the 16S rRNA gene were amplified using barcoded ITS1F/ITS2 and F515/R806 primers, respectively, according to Earth Microbiome Project's protocols. Fungal ITS and bacterial 16S primers were made available through the Alfred P. Sloan Foundation Built.</p> <p>Sequencing (2x300 bp) has been performed on Illumina Miseq platform at University of California Riverside (UCR). Data analyses were performed on the High-Performance Computing Cluster at UCR in the Institute of Integrative Genome Biology.</p> <p>The dataset consists of 2 zip archives. Here is a summary of their contents:</p> <ul> <li>ITS_fungi: R1.fastq and <em>R2</em><em>.</em>fastq files</li> <li>16S_bacteria: R1.fastq and <em>R2</em><em>.</em>fastq files</li> </ul>
An amplicon sequencing protocol for attacker identification from DNA traces left on artificial prey
<ol> <li>Clay model studies are a popular tool to identify predator-prey interactions that are challenging to observe directly in the field. But despite its wide use, the method's applicability is limited by its low taxonomic resolution. Attack marks on clay models are usually identified visually, which only allows classification into higher taxonomic levels of predators. Thus, the method is often biased, lacks proof and, above all, standardization.</li> <li>Here, we tested whether precise identification of attackers can be provided by amplification and sequencing of mitochondrial DNA left in bite marks on clay models. We validated our approach in a controlled laboratory study as well as in a field experiment using clay models of a common European amphibian, the European fire salamander (<i>Salamandra salamandra</i>). DNA based taxonomic assignments were additionally compared to visual assessments of bite marks.</li> <li>We show that trace DNA of attackers can be routinely isolated and sequenced from bite marks, providing accurate species level classification. In contrast, visual identification alone yielded a high number of unassigned predator taxa. We also highlight the sensitivity of the method and show likely sources of contamination as well as probable cases of secondary and indirect predation.</li> <li>Our standardized approach for species level attacker identification opens up new possibilities far beyond the standard use of clay models to date, including food web studies at unprecedented detail, invasive species monitoring as well as biodiversity inventories.</li> </ol>
PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets
<p>Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. </p> <p>Available datasets: </p> <p>- reference file for regions selected for amplicon sequencing: <em>Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa</em></p> <p>- final .bam files containing processed PacBio sequencing reads aligned to the reference:</p> <p><em>PacBio_amplicon_seq_T1.bam</em> and <em>PacBio_amplicon_seq_T6.bam</em> </p> <p>- . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: </p> <p><em>P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table</em> and <em>P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table</em></p> <p>Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%). Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.</p>
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.