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Dataset results
200 results for “Genomic Resources”
Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations
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Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013
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Data from: "White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 June 2013-31 July 2013
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Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
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Leveraging genetic resources and genomic prediction to enhance flavonol content in cranberry fruit
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Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
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Data from: Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources
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Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array
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Data from: "Transcriptome resources for three hybrid sunflower species (Helianthus anomalus, H. deserticola, H paradoxus)" in Genomic Resources Notes accepted 1 February 2013–31 March 2013
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Data from: "Characterization of two Iberian freshwater fish transcriptomes, Squalius carolitertii and Squalius torgalensis, living in distinct environmental conditions" in Genomic Resources Notes Accepted 1 April 2015 to 31 May 2015
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Data from: "Transcriptomic resources for Hazelnut tree (Corylus avellana L.)" in Genomic Resources Notes Accepted 1 August 2015 to 31 September 2015
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A genomics resource for genetics, physiology, and breeding of West African sorghum
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Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources
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Data from: "Transcriptome resources for the oriental rat flea and primary plague vector, Xenopsylla cheopis" in Genomic Resources Notes Accepted 1 August 2015 to 31 September 2015
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Data from: Development of a genomic resource and quantitative trait loci mapping of male calling traits in the lesser wax moth, Achroia grisella
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Data from: "Transcriptomic resources for three populations of Conus miliaris (Mollusca: Conidae) from Easter Island, American Samoa and Guam" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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YAMP Resources with Human Genome indexed bbmap 38.76
<p>Resource dataset for <strong>YAMP</strong> (https://github.com/alesssia/YAMP) with Human Genome indexed using <strong> bbmap 38.76</strong></p> <p><em>Original dataset:</em></p> <p>Alessia. (2017). Data for YAMP (https://github.com/alesssia/YAMP) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1068229</p> <p><em>From the original dataset :</em></p> <p>This dataset includes all the databases/datasets queried by YAMP (https://github.com/alesssia/YAMP). This dataset has been created to help the users to get started with YAMP, and to save them from the hassle of collecting and downloading the data from different sources.</p> <p>More in details, this dataset contains:</p> <ul> <li>a FASTA file listing the adapter sequences to remove in the trimming step. This file is usually provided within the BBmap installation (https://sourceforge.net/projects/bbmap, version 37.68). </li> <li>two FASTA files describing synthetic contaminants (sequencing_artifacts.fa.gz and phix174_ill.ref.fa.gz). These files are usually provided within the BBmap installation (https://sourceforge.net/projects/bbmap, version 37.68). </li> <li>a FASTA file provided by Brian Bushnell for removing human contamination (described here: http://seqanswers.com/forums/showthread.php?t=42552). Please note that this file should be indexed beforehand. This can be done using BBMap, using the following command: `bbmap.sh -Xmx24G ref=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz`. </li> <li>the BowTie2 database file for MetaPhlAn2. This file is usually provided within the MetaPhlAn2 installation (version 2.6.0)</li> <li>the ChocoPhlAn and UniRef (Uniref50, Uniref90) databases, downloaded directly by HUMAnN2 (version 0.9.9), as explained here: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-5-download-the-databases</li> </ul>
A chromosome-scale genome assembly resource for Myriosclerotinia sulcatula infecting sedge grass (Carex sp.)
<p>The fungus <em>Myriosclerotinia sulcatula</em> is a close relative of the notorious polyphagous plant pathogens <em>Botrytis cinerea</em> and <em>Sclerotinia sclerotiorum</em> but exhibits a host range restricted to plants from the <em>Carex</em>genus (<em>Cyperaceae</em> family). To date, there are no genomic resources available for fungi in the <em>Myriosclerotinia</em>genus. Here, we present a chromosome-scale reference genome assembly for <em>M. sulcatula</em>. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N<sub>50</sub> of 2,649.7 kbp and N<sub>90</sub> of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for <em>M. sulcatula</em> as a resource for studying evolution and pathogenicity in fungi from the <em>Sclerotiniaceae</em> family. </p>
Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback
Many generalist species consist of specialized individuals that use different resources. This within-population niche variation can stabilize population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favor ecological diversity (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate-sized lakes support generalist stickleback populations using an even mixture of the two prey types, due to greater among-individual variation in diet and morphology. In contrast, genomic diversity increases with lake size. Thus, phenotypic diversity and neutral genetic polymorphism are decoupled: trophic diversity being greatest in intermediate-sized lakes with high resource diversity, whereas neutral genetic diversity is greatest in the largest lakes.
Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms
Assessing the genetic variability of the tick Ixodes ricinus - an important vector of pathogens in Europe - is an essential step for setting-up anti-tick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, carried out by applying a genomic complexity reduction step, followed by pyrosequencing and the use new bioinformatics tools. Almost 1.4 million reads (average length : 528 nt) were generated with a full Roche 454 GS FLX run on two Reduced Representation Libraries of I. ricinus. 321,088 putative SNPs were isolated using the newly developed bioinformatics tool READ2SNPS, which identifies SNPs without requiring a reference genome. Stringent selection criteria were applied in a bioinformatics pipeline to select 1,768 SNPs for the development of specific primers. Among 384 randomly selected SNPs, tested by Fluidigm genotyping technology on 464 individual ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on 6 natural populations of ticks showed that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiencies. The generated SNP resource described here will be useful for a variety of applications such as the assessment of the genetic structure of I. ricinus populations.
ScienceDex guides
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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.