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.
83
datasets available to search
ShareScore release 0.7.1
Dataset results
83 results for “microsatellite loci”
Arctic grayling neutral genomic microsatellite loci from the Kuparuk, the Sagavanirktok (primarily Oksrukuyik Creek) and the Itkillik (primarily the I-Minus outlet stream) watersheds, 2010-2014
Since 2009, The FISHSCAPE Project (National Science Foundation grants: 1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream), The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Atigun River and Tea and Galbraith Lakes), and Itkillik (primarily the I-Minus outlet stream a tributary that that feeds into the Itkilik River). Goals of the FISHSCAPE project are to understand and predict the adaptability and persistence of a key Arctic species, the Arctic grayling (Thymallus arcticus), to changing climate and hydrology. Research questions include: (1) Does landscape structure determine movement within and among watersheds; (2) do populations adapt to stream characteristics at local and regional scales; and (3) will the relative adaptability of populations determine their persistence under future climate change. We used genetics to investigate population structure and landscape genetics for Arctic grayling. Adult and young-of-the-year fish were captured at sampling locations and coordinates and/or specific station locations were noted. Fin clip samples (adults) or whole fish (young-of-the-year) were collected and preserved in 95% ethanol until Deoxyribonucleic acid (DNA) was extracted. Polymerase chain reaction (PCR) products from neutral genomic microsatellite loci were scored and used to assess population genetic structure and other population parameters. Adult capture and movement data, including length, weight and Passive Integrated Transponder (PIT) tag information, can be found in a separate data package.
FIGURE 1 in Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)
FIGURE 1 | Sampling sites of Pseudopimelodus magnus and P. atricaudus in the middle and lower sectors of the Cauca River.
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 on sample A1-F1-07, Family A1. Both reactions were run simultaneously on the same fragment analysis plate using the same PCR conditions, DNA concentrations, and dilution factor. a) Chromatograph of progeny exhibiting an allele call of 74/74. Parents are 74/76 and 76/76. The observed 76 bp peak was considered to be weak. Cloning and sequencing confirmed the existence of this 76 bp fragment. b) Chromatograph of the same progeny as in Fig. 2a now exhibiting an allele call of 72/74 afer primer modification. Parents are now 72/74 and 74/74. The observed 74 bp peak is more pronounced compared to the previous 76 bp call. The intensity of the 74 bp peak also increased while the other 3 visible peaks decreased. This suggests an increase in adenylation has occurred.
Fig. 1 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 1. Sequence alignment of Ccmic3 with original primer design. Top two sequences are genotypes of 74 bp allele and bottom two sequences are genotypes of the 76 bp allele. One extra thymine residue on the 5' end appeared in 8 of the 8 clones for this allele leading to difficulties in scoring this locus. Redesign of the forward primer by adding the extra guanines provided better resolution in scoring. Lower case sequence represents the Topo 2.1 vector just past the EcoRI in the multiple cloning site.
Fig. 3 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 3. Comparing artifactual bands to actual bands to determine allele as observed at the Ccmic25 locus. a) Chromatograph of sample exhibiting an artifactual band can be observed at the 136 bp peak. The geometric shape and configuration is not consistent with those of microsatellites. b) This chromatograph shows the characteristic high peak followed by a low peak expected when making a call around the 137 bp peak. To the lef of both peaks are very low broad bands, commonly observed during analysis. In homozygote individuals, these peaks may extend higher and resemble an artifactual band similar to what was observed in Fig. 3a.
Fig. 2 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 2. Locations of sampling for tissue (1. Hoengseong-gun, Gangwon-do, 2. Uljin-gun, Gyeongsangbuk-do, 3. Jeongeup-si, Jeollabukdo, 4. Muju-gun, Jeollabuk-do, 5. Hampyeong-gun, Jeollanam-do).
Fig. 1. Maximum likelihood tree generating from a 399 in Isolation and Characterization of Polymorphic Microsatellite Loci for Caridina cantonensis and Transferability Across Eight Confamilial Species (Atyidae, Decapoda)
Fig. 1. Maximum likelihood tree generating from a 399-bp long COI dataset (GenBank accession no. MH176649-MH176993). SH-alrt/ bootstrap support values are indicated at major nodes. Each coloured notation represents one species.
FIGURE 2 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 2 | Discriminant analysis of principal components for nine microsatellite loci and 138 individuals of Pimelodus yuma in three sections (S4/5, S6 and S7/8) of the Cauca River.
FIGURE 1 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 1 | Studied sampling sites of Pimelodus yuma along the lower sections (S4–S8) of the Cauca River. The pentagons indicate sampling sites in floodplain lakes and the stars indicate sites along the main channel of the river.
FIGURE 2 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 2 | Results of Structure (A, B) and Discriminant analysis of principal components (C) for Pseudoplatystoma magdaleniatum. A: K = 1; B: K = 2; M: Margento, PC: Punta Cartagena, PB: Puerto Berrío, SN: Samaná Norte.
FIGURE 3 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 3 | STRUCTURE results for Pimelodus yuma showing K= 2 genetic stocks in three sections (S4/5, S6 and S7/8) of the Cauca River.
Fig. 1 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 1. Spraints collection sites along Ungokcheon Stream, Bonghwa-gun, Gyeongsangbuk-do.
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
FIGURE 1 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 1 | Sampling sites of Pseudoplatystoma magdaleniatum in the Magdalena-Cauca basin.
Population genetic structure of Nephrops norvegicus from the Adriatic Sea inferred using microsatellite loci
Open the record for dataset details and reuse information.
Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird
Open the record for dataset details and reuse information.
Microsatellite loci genotypes dataset (N=121 unique individuals) from: Sex-mediated gene flow of grayfoot chacma baboons (Papio ursinus griseipes ) in a highly seasonal habitat of Gorongosa National Park, Mozambique
Open the record for dataset details and reuse information.
Data from: Analysis of microsatellite loci in tree of heaven (Ailanthus altissima (Mill.) Swingle) using SSR-GBS
Microsatellite markers are still the marker of choice for many research questions in the field of forest genetics. However, the number of available markers is often low for species that have not been studied intensively like the tree of heaven (Ailanthus altissima). During the last decade, next generation sequencing (NGS) has offered advanced techniques for efficiently identifying microsatellite markers and accurately genotyping samples. Here, we identify new microsatellite markers for the tree of heaven by applying an NGS-based method using the Illumina MiSeq platform. NGS technology was proved to be an effective method for fast and cost-efficient identification of microsatellite markers by implementing a genotyping-by-sequencing approach based on Illumina amplicon sequencing (SSR-GBS). We screened three populations from Eastern Austria for genetic variation at 19 newly identified microsatellite loci. We tested two different genotyping approaches: (1) considering only allele lengths (forming a so-called 'allele length dataset'), (2) taking also single nucleotide polymorphisms (SNPs) within the amplified fragments into account (forming a so-called 'SNP dataset'). The results revealed higher values for all genetic diversity parameters, as well as a better resolution of genetic assignment, when the latter approach was followed. Thus, by taking advantage of sequence information which is provided by SSR-GBS, one may achieve considerable gains in performance using the same marker set. The developed markers provide a cost-efficient tool for genotyping populations of tree of heaven and the approach presented here promises to be of high value for medium throughput genotyping applications in non-model forest tree species. We will use this method to widen the perspectives for further population genetic investigations of the tree of heaven.
Data from: Population genetic analyses using 10 new polymorphic microsatellite loci confirms genetic subdivision within the olm, Proteus anguinus
We provide a comparative population genetic study of the elusive amphibian, Proteus anguinus, by comparing the genetic diversity and divergence among four cave populations (96 individuals) sampled in the Dinaric Karst of Croatia. We developed 10 variable microsatellite markers using pyrosequencing and applied them to the four selected populations belonging to four different cave systems. The results showed strong genetic differentiation between the four caves corroborating with previous findings suggesting that Proteus might comprises several unrecognized taxa. Our results confirmed that gene flow should be high within the caves, whereas it is low between hydrographic systems since geological periods. Finally, we conclude that the high genetic subdivision suggests the necessity of treating the four studied Proteus populations as evolutionary significant units.
Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites' performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.
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.