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.
1,696
datasets available to search
ShareScore release 0.9.0
Dataset results
1,696 results for “DNA sequence”
Supplementary material 1 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Details on the fungal genomes/contigs targeted : Data type: Excel spreadsheet
Supplementary material 2 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
The 86 multiple sequence alignments used : Data type: Text
Figure 2 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 2 - Public fungal ITS sequences are subjected to insufficient trimming in their distal ends. Panel a shows the dissimilarity (y-axis) as a function of the relative sequence position (x-axis). The plot is based on 10,584 sequences from 86 species. Panel b and c show zoom-ins of the 5' and 3' ends, respectively. Dashed lines indicate point-wise standard errors.
Figure 1 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 1 - Example of poorly trimmed sequences (sequence four and on) from the species Setosphaeria turcica. The 5' end of the alignment is shown, and the poorly trimmed sequences cover the last ~5 bases of SSU and the immediate start of ITS1. The topmost sequence is genome-derived, and sequences two and three are regular Sanger sequences retrieved from the INSDC from other studies than the one with the poorly trimmed sequences (sequences four and on). SeaView v. 4 (Gouy et al. 2010) was used to visualize the alignment.
Figure 3 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 3 - The proportion of poorly trimmed (y-axis) fungal ITS sequences submitted to the INSDC does not decrease over time (x-axis). The regression line (dashed), which was derived by overdispersed Poisson rate regression, shows a weak but significant increasing trend (yearly relative increase of 0.047, p=0.0291).
Figure 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Figure 1 - The mitochondrial genome of Pontoscolex corethrurus (Müller, 1857). Gene order and positions are shown, including the putative control region. IUPAC single letter codes are used to identify transfer RNA. The L1, L2, S1, and S2 transfer RNAs are differentiated on the basis of their anti-codons TAG, TAA, TCT, and TGA, respectively.
Figure 2 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Figure 2 - Phylogenetic relationships among phylum Annelida based on the combined 13,416 bp nucleotide positions. Total alignment length is greater than the combined P. corethrurus protein coding and rRNA sequence lengths due to overlapping protein coding sequences that are subsequently concatenated, and indel regions in the alignment. The posterior probability value of BI analyses and bootstrap support values of ML analyses (in the order: BI, ML) are indicated near the branches.
Supplementary material 3 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing. Metabarcoding and Metagenomics 1: e13709. https://doi.org/10.3897/mbmg.1.13709
Exploratory statistics addressing sequencing depth per country and MOTU rarefaction.
Supplementary material 2 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing. Metabarcoding and Metagenomics 1: e13709. https://doi.org/10.3897/mbmg.1.13709
Supporting Information 2
Figure 1 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Figure 1 - Surstyli (dorsal view) for male Themira biloba (A) and Themira "biloba-like" (B). Red arrows indicate basal process on left surstylus; green arrow for basal process on right surstylus.
Figure 3 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Figure 3 - Adult female (A–H), showing lateral (A) and dorsal (B) views of habitus (sans abdomen), anterior (C) and ventral (D) views of head capsule, anterior and posterior views of fore leg (E), mid leg (F) and rear leg (G), and ventral view of abdomen (H).
Figure 2 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Figure 2 - Adult male (A–M), showing lateral (A) and dorsal (B) views of habitus, anterior (C) and ventral (D) views of head capsule, anterior and posterior views of fore leg (E), mid leg (F) and rear leg (G); ventral view of abdomen (H) showing modified 4th sternites; anterior (I), dorsal (J), left (K) and right (L) views of hypopygium, as well as various views of the penis (M).
Healthy and cancer individuals from Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer
<p>Oxford Nanopore sequencing data from 61 samples described in manuscript "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer"<br><br></p> <p>All data are aligned to UCSC analysisSet hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/), and use 0-based coordinates.</p> <p><strong>Level 2:</strong> In order to provide combined fragmentation and methylation information, Biscuit was used to create “epiBED” files (see Methods). epiBED files contain each read on a separate line, with each DNA methylation call on the read. epiBED files can be used for combined methylation/fragmentomic analysis, and are compatible with the CelFiE-ISH software that was used for cell of origin deconvolution.</p> <p>Creation of Biscuit EpiBED files:<br>Biscuit (https://huishenlab.github.io/biscuit/) v. 1.4.1-dev was used with the command “biscuit epiread -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 1000000 hg38.analysisSet.fa”, where the reference is the same UCSC reference genome used for alignment. Files are available in the Zenodo repository listed in Data Availability.</p> <p><strong>Level 3</strong>: DNA methylation BED files. BED files created by modkit (see Methods) provide one line for each CpG covered, and can be used for basic DNA methylation analysis.<br><br>Creation of modkit BED files:<br>BED files were created using modkit (https://github.com/nanoporetech/modkit) v. 0.1.5 with the command “modkit pileup --cpg --combine-strands --ignore h --filter-threshold 0.9 --bedgraph". </p> <p> </p>
Fig. 1. MtCOI sequence comparison for Spodoptera litura and S. exigua. A in DNA barcoding and phylogenetic relationships of Spodoptera litura and S. exigua (Lepidoptera: Noctuidae)
Fig. 1. MtCOI sequence comparison for Spodoptera litura and S. exigua. A color version of this graphic can be seen online in supplementary material for this article in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
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
Figure 4 from: Binh HT, Ngoc NV, Tagane S, Toyama H, Mase K, Mitsuyuki C, Strijk JS, Suyama Y, Yahara T (2018) A taxonomic study of Quercus langbianensis complex based on morphology, and DNA barcodes of classic and next generation sequences. PhytoKeys 95: 37-70. https://doi.org/10.3897/phytokeys.95.21126
Figure 4 Comparison of Q. langbianensis complex between NJ tree (left, Clade M3 of Fig. 3) and Bayesian tree (right: Clade 2 of Fig. 2).
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.