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2,848 results for “sequence data”
data & analysis scripts of " Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"
<p>Analysis scripts and data accompanying the manuscript "Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"</p>
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
<p>The data presented in "NanoGalaxy: A Galaxy tool kit with workflows for third-generation sequence analysis" to illustrate the functionality of the tools was obtained from: Wick, Ryan R., et al. "Completing bacterial genome assemblies with multiplex MinION sequencing." <em>Microbial genomics</em> 3.10 (2017).</p> <p>+</p> <p>Li, Ruichao, et al. "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data." <em>Gigascience</em> 7.3 (2018): gix132.</p>
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
The data of complete chloroplast genome sequence of Sorbus amabilis (Rosaceae) in China
<p>This dataset includes the complete chloroplast genome of <em>Sorbus amabilis </em> in China.</p>
FIGURE 32 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURE 32. Neighbor joining tree showing the clustering of similar COI sequences in Cyclocephala taxa. Parentheses after the taxon name indicate the number of sequences represented in that cluster. Parentheses are followed by a three-letter country code. CRI = Costa Rica, GLP = Guadeloupe, GTM = Guatemala, HND = Honduras, KNA = St. Kitts and Nevis, MEX = Mexico, NIC = Nicaragua, PAN = Panama, SLV = El Salvador, VEN = Venezuela. Colored branches highlight taxa of the C. mafaffa species complex (green = C. deceptor; red = C. mafaffa mafaffa; blue = C. mafaffa grandis).
FIGURES 25–30 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 25–30. Stigmalia deficiens Casey, lectotype male and paralectotype female. 25, Stigmalia deficiens Casey lectotype male, dorsal habitus. 26, Stigmalia deficiens Casey paralectotype female, dorsal habitus. 27, Parameres of lectotype male, caudal view. 28, Aedeagus of lectotype male, lateral view. 29, Lectotype male specimen labels. 30, paralectotype female specimen labels.
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17, Stigmalia cuernavacana Casey holotype female, dorsal habitus. 18, Elytral epipleural flange of holotype female, dorsal view. 19, Elytral epipleural flange of holotype female, lateral view. 20, Holotype female specimen labels.
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21, Stigmalia fallaciosa Casey holotype male, dorsal habitus. 22, Parameres of holotype male, caudal view. 23, Aedeagus of holotype male, lateral view. 24, Holotype male specimen labels.
FIGURES 11–16 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 11–16. Stigmalia deceptor Casey, lectotype male and paralectotype female. 11, Stigmalia deceptor Casey lectotype male, dorsal habitus. 12, Stigmalia deceptor Casey paralectotype female, dorsal habitus. 13, Parameres of lectotype male, caudal view. 14, Aedeagus of lectotype male, lateral view. 15, Lectotype male specimen labels. 16, Paralectotype female specimen labels.
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7, Stigmalia mafaffa histrionica Casey holotype female, dorsal habitus. 8, Holotype female, elytral epipleural flange in dorsal view. 9, Holotype female, elytral epipleural flange in lateral view. 10, Holotype female specimen labels.
FIGURES 1–2. Cyclocephala deceptor and C in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 1–2. Cyclocephala deceptor and C. mafaffa, basal margin of the pronotum. 1, Cyclocephala deceptor with pronotal basal bead medially complete. 2, Cyclocephala mafaffa with pronotal basal bead medially incomplete.
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3, Lectotype male, dorsal habitus. 4, Lectotype male, ventral habitus. 5, Lectotype male, lateral habitus. 6, Lectotype male specimen labels and aedeagus. Photographs courtesy of Matthias Seidel (Department of Entomology, National Museum, Prague, Czech Republic).
Data sets for: EMA-amplicon-based sequencing of untreated and SODIS treated rainwater
<p>Data sets for the EMA-amplicon-based sequencing of untreated and treated rainwater collected from an informal settlement and rural farming community in South Africa. The data sets were used for the publication: EMA-amplicon-based sequencing informs risk assessment analysis of water treatment systems (Submitted to Science of the Total Environment).</p>
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
Data: An ESCRT-III polymerization sequence drives membrane deformation and fission
<p>Raw data to "an ESCRT-III polymerization sequence drives membrane deformation and fission"</p>
Automated identification of the mouse brain's spatial compartments from in situ sequencing data
<p>Example data [1] for testing in situ sequencing graph-based decoding pipeline and decoding results for reproducing publication analyses. Image decoding pipeline and notebooks are available at: <a href="https://github.com/wahlby-lab/graph-iss">https://github.com/wahlby-lab/graph-iss</a></p> <p>------------</p> <p>[1] Ke, Rongqin, et al. "In situ sequencing for RNA analysis in preserved tissue and cells." <em>Nature methods</em> 10.9 (2013): 857.</p>
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
Data from: Transcriptome sequencing reveals signatures of positive selection in the spot-tailed earless lizard
<p><span><span><span><span><span><span><span><span><span><span><span>The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (<i>Holbrookia lacerata</i>)<i> </i>and Southern Spot-Tailed Earless Lizard (<i>Holbrookia</i> <i>subcaudalis</i>), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (<i>Holbrookia maculata</i>). Our efforts produced high quality and robust transcriptome assemblies validated by <b>1</b>) quantifying the number of processed reads represented in the transcriptome assembly and <b>2</b>) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three <i>Holbrookia </i>species, <i>Anolis carolinensis</i>, and <i>Sceloporus undulatus</i>. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the <i>Holbrookia</i> lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern <i>H. lacerata</i> and Southern <i>H.</i> <i>subcaudalis </i>that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species<i>.</i></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status
<p>Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (<em>Crotalus oreganus</em>) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.</p>
Didimosphenia geminata: sequences and morphology data set
<p><span>Microalgae and their invasiveness are recurrent themes in aquatic environments and many invasions by microalgae are linked to eutrophication. However the diatom <i>Didymosphenia geminata </i>has gained notoriety in forming thick mucilaginous mats in pristine, rocky-bottomed rivers with no obvious connection to elevated levels of nutrients. This species is native to freshwaters of the circumboreal region of the Northern Hemisphere and blooms in the Southern Hemisphere have been attributed to recent introductions of the species to these regions. Although regional population genetic analyses have suggested multiple recent introduction of this species, the gene flow and the spatial genetic diversity distribution on a global scale remains unknown. We develop a phylogeographic analysis to investigate the genetic diversity of <i>D. geminata</i> populations around the globe. Our results indicate two distinct genetic lineages geographically distributed that remain spatially isolated. One lineage is exclusively found in Europe, the other is distributed in North America, New Zealand and South America. Since blooms of <i>D. geminata</i> commenced in North America and in Europe simultaneously, these data support the idea that factors associated with global environmental change and possibly the associated biome are the cause of blooms globally. We further discuss the role of human mediated-dispersal.</span></p>
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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.