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.
281
datasets available to search
ShareScore release 0.9.0
Dataset results
281 results for “genetic sequence”
Figure 1 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing
Figure 1. Map of geographical locations of research sites.
Fig. 3 in Prevalence of a new genetic group, MEAM-K, of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Karnataka, India, as evident from mtCOI sequences
Fig. 3. Graph indicating net evolutionary divergence between groups of sequences.
Fig. 1 in Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach
Fig. 1. Map showing Melbourne's water catchment areas where samples were collected (2009-2022).
Fig. 1 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America
Fig. 1. Halyomorpha halys collection sites in Korea and the USA.
Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for non-model organisms, potentially revolutionising the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (1) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci, and; (2) quantify error rates for loci, alleles and SNPs. As an empirical example we use a double digest RAD dataset of a non-model plant species, Berberis alpina, collected from high altitude mountains in Mexico.
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES
<p>Appendix 1 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others.</p> <p>Appendix 2 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022).</p> <p>Appendix 3 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample").</p> <p>Appendix 4 Position of IS<em>6110</em> insertion sites in the panel of <em>Mycobacterium bovis </em>strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the reference genome AF2122/97.</p> <p>Appendix 5 Position of IS<em>6110</em> insertion sites in the <em>Mycobacterium bovis </em>strain panel of SB0120-DHV. Position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the Mb3601 reference genome.</p> <p>Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.</p>
Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES
<p>Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric.</p> <p>Annex S2: Pan-genomic study performed on 12 <em>M. bovis</em> complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence.</p> <p>Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS<em>6110</em> is marked in green. "Indel distribution" sheet shows the indel distribution on the <em>M. bovis</em> genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found.</p> <p>Annex S4: WgSNP analysis performed on 98 <em>M. bovis</em>. SNPs were annotated and selected according to their specificity to an <em>M. bovis</em> group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position.</p> <p>Annex S5: Alignments of the 12 <em>M. bovis </em>complete genomes.</p>
TRIAGE-GS: Towards Reducing Inefficiencies Affecting Genetics Encounters Through Genome Sequencing
ClinicalTrials.gov study NCT06935019. IPD Sharing: YES. Countries: 1. Publications: 1.
Establishing a robust genetic sequencing and gene expression data library in cardiovascularly healthy cats
Open the record for dataset details and reuse information.
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
Open the record for dataset details and reuse information.
A genotype-by-sequencing dataset and identity-by-state matrix of genetic variation in Pinus radiata from 16 counties
Open the record for dataset details and reuse information.
Single cell RNA sequencing provides clues for the developmental genetic basis of Syngnathidae’s evolutionary adaptations
Open the record for dataset details and reuse information.
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Open the record for dataset details and reuse information.
Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Open the record for dataset details and reuse information.
Data from: Reduced representation sequencing reveals weak genetic differentiation between Canadian and European Larus hyperboreus (Glaucous Gull)
Open the record for dataset details and reuse information.
Amplicon sequencing data for genetic variants at the ASIP locus that determine grey and black fur of the brushtail possum
Open the record for dataset details and reuse information.
Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples
Open the record for dataset details and reuse information.
Data from: Genetic structure and demographic history of house mice in Western Europe inferred using whole genome sequences
Open the record for dataset details and reuse information.
Data from: Whole genome sequencing reveals clade-specific genetic variation in blacklegged ticks
Open the record for dataset details and reuse information.
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.