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36 results for “marker discovery”
Code and data for "Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer".
<p>Code and data for "<strong>Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer</strong>".</p> <ul> <li> <p>The publicly available datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository (<a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a>) and UCSC Xena Browser (TCGA, <a href="https://xena.ucsc.edu/">https://xena.ucsc.edu/</a>).</p> </li> </ul>
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
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Data from: Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)
The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is threatened by habitat destruction, over-harvest and hybridization with nonnative trout. Currently, three Geographic Management Units (GMUs) are recognized within the taxon. Here, we describe a suite of 68 single-nucleotide polymorphism (SNP) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout (O. c. seleneris). These include markers variable within the two subspecies (n = 35), diagnostic for the two subspecies (n = 23) and diagnostic for Yellowstone cutthroat trout (O. c. bouvieri) and other closely related subspecies (n = 10). Sixty-three markers were discovered by Sanger sequencing of 171 EST loci in an ascertainment panel including Lahontan cutthroat trout from four populations representing all GMUs. Five markers were identified in a secondary sequencing effort with a single population of Lahontan cutthroat trout. TaqMan assays were validated on six Lahontan cutthroat trout populations and a diverse panel of other trout. Over 90% of the markers variable in Lahontan cutthroat trout were polymorphic in at least two populations, and 66% were variable within all three GMUs. All Lahontan diagnostic markers were also fixed for the Lahontan allele in Paiute cutthroat trout. Most of the Yellowstone diagnostic markers can also be used for this purpose in other cutthroat trout subspecies. This is the first set of SNP markers to be developed for Lahontan cutthroat trout, and will be an important tool for conservation and management.
Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.
Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84,937 contigs representing approximately 18,282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multi-locus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.
Figure 8 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 8. Diet molecular phylogenetic inference for Arsipoda spp. Synthetic trees showing the phylogenetic placement of trnL(UAA) sequences obtained from (A, C) Arsipoda isola Samuelson and (B) Arsipoda geographica Gómez-Zurita sp. nov. (see main text for details).
Figure 6 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 6. Aedeagus (dorsal, lateral and ventral views) of Arsipoda geographica Gómez-Zurita sp. nov.
Figure 3 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 3. Spermathecae of (A) Arsipoda agalma Samuelson and of (B) Arsipoda geographica Gómez-Zurita sp. nov.
Figure 4 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 4. (A) Holotype of Arsipoda geographica Gómez-Zurita sp. nov. (male). (B) Holotype of Arsipoda rostrata Gómez-Zurita sp. nov. (male). Scale bar = 1 mm.
Figure 2 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 2. Mitochondrial phylogeny of New Caledonian Arsipoda Erichson. (A) Arsipoda agalma Samuelson, a representative New Caledonian species (scale bar = 1 mm). (B) Most parsimonious tree for mitochondrial DNA data of New Caledonian Arsipoda with bootstrap support measures in unweighted (above branches) and weighted (below branches) analyses, treating gaps as missing data (top value) or a fifth character state (bottom value). (C) Best topology of maximum likelihood analysis for the same data showing bootstrap support values.
Figure 1 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 1. Distribution of Arsipoda Erichson in New Caledonia (from Samuelson, 1973) and geographic source of samples available for phylogenetic analysis with locality data as in Table 1.
Data from: Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii
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Data from: Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)
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Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.
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Data from: DISCOMARK: nuclear marker discovery from orthologous sequences using draft genome data
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Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)
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Data from: Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery
Premise of the study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. Methods and Results: A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus. Conclusions: This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.
Data from: De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing.
Recent developments in sequencing technologies and bioinformatics analyses provide an unprecedented opportunity for cost and time effective high quality microsatellite marker discovery in non-model organisms for which no genomic information is available. Here, we use shotgun pyrosequencing of a microsatellite-enriched library to develop, for the first time, microsatellite markers for Alnus glutinosa, a keystone tree species of European riparian woodland communities. From a total of 17,855 short sequences, we identified 590 perfect microsatellites from which 392 had designed primers. A subset of 48 loci were tested for amplification, twelve of which were polymorphic in A. glutinosa. These twelve loci were successfully co-amplified in a single multiplex PCR experiment and validated for population genetics applications. In addition, ten and eight of these microsatellites were found to be transferable to the related A. incana and A. cordata species. The developed multiplex of 12 microsatellite markers therefore provides new opportunities for experimental evolutionary and forest genetics research in Alnus.
Figure 7 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 7. Aedeagus dorsal, lateral and ventral views of Arsipoda rostrata Gómez-Zurita sp. nov.
Figure 5 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 5. Pronotum of Arsipoda geographica Gómez-Zurita sp. nov.
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.