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.
120
datasets available to search
ShareScore release 0.9.0
Dataset results
120 results for “barcode sequence”
TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing
Open the record for dataset details and reuse information.
Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1–4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an 'in silico' method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low-coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low-coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
Figure 9 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 9 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Julida. Note well-supported COI groups for each species allowing for sequence-based species identification. Numbers above and below branches show bootstrap values of NJ analysis, branch length indicates sequence divergence in %.
Figure 8 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 8 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Polyxenida, Polydesmida and Glomerida. Solid circles: examples of excellent resolution of very close species of the genus Polydesmus. Numbers above and below branches show bootstrap values of NJ analysis, branch length indicates sequence divergence in %.
Figure 11 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 11 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Chilopoda. Asterisks: Deep divergences within Lithobius tricuspis and Lithobius mutabilis suggesting cryptic speciation. Numbers above and below branches show bootstrap values of neighbour-joining analysis, branch length indicates sequence divergence in %.
Figure 7 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 7 - Complete neighbour-joining tree of COI sequence divergences (K2P model) of studied myriapod orders; barcoded terminal taxa and clades above their basal nodes omitted. This tree serves for orientation in the detailed trees given in Figs 8–11.
Figure 1 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 1 - Map of sampled areas (dots). For checks of intraspecific variability of COI sequences, localities in Bavaria, but also elsewhere within the species' areas of distribution, have been sampled and analyzed (sampling data from November 2008 to November 2010; a few specimens from northern Spain omitted).
Figure 2 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 2 - Some Bavarian myriapods for which barcodes are now available. A. Glomeris pustulata Latreille, 1804. B. Polydesmus helveticus Verhoeff, 1894. C. Cylindroiulus boleti (C. L. Koch, 1847). D. Unciger foetidus (C. L. Koch, 1838). E. Haasea flavescens (Latzel, 1884). F. Atractosoma meridionale Fanzago, 1876. G. Cryptops parisi Brölemann, 1920. H. Henia vesuviana (Newport, 1845). Photos: J. Spelda.
Figure 10 from: Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123-139. https://doi.org/10.3897/zookeys.156.2176
Figure 10 - Neighbour-joining tree of COI sequence divergences (K2P model) of studied Chordeumatida. Asterisk: deep barcoding divergence in Chordeuma silvestre; solid squares: polyphyly of genus Ochogona; arrows: low sequence divergences in the genera Craspedosoma, Listrocheiritium and Rhymogona. Numbers above and below branches show bootstrap values of NJ analysis, branch length indicates sequence divergence in %.
Data from: Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
Open the record for dataset details and reuse information.
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Open the record for dataset details and reuse information.
Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
Open the record for dataset details and reuse information.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Open the record for dataset details and reuse information.
Data from: DNA barcodes from century-old type specimens using next generation sequencing
Open the record for dataset details and reuse information.
Data from: Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens
Open the record for dataset details and reuse information.
Epigenetic age-predictions in mice using pyrosequencing, droplet digital PCR or barcoded bisulfite amplicon sequencing
GEO Series GSE156193. Mus musculus. 111 samples. Type: Methylation profiling by high throughput sequencing.
Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes
GEO Series GSE96583. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
GEO Series GSE125162. Saccharomyces cerevisiae. 12 samples. Type: Expression profiling by high throughput sequencing.
Targeted DNA sequencing of barcoded SUM159PT cells
GEO Series GSE221495. Homo sapiens. 47 samples. Type: Other.
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.