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.
738
datasets available to search
ShareScore release 0.9.0
Dataset results
738 results for “Microsatellite”
RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results
<p>Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g., paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (RADseq) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (<em>Microcebus murinus</em> and <em>M</em>. <em>griseorufus</em>). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a cautionary tale for the inference of interspecific hybridization with microsatellite data.</p>
Desert tortoise scat microsatellite results
<p>Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce logistical challenges, ecological impacts, and zoonotic risks. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success, defined as ≥9 loci with amplification varied by species: 15% of samples for Agassiz's desert tortoise and 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. Fragments up to 400 bp for tortoises and 980 bp for chuckwallas were successfully recovered from scat swab samples. This study demonstrates that genotypes can successfully be obtained from swabs of herbivorous reptile scat collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for estimating population genetic parameters.</p>
Supplementary material 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 5: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae and Bactrocera dorsalis populations. The highest Betweenness-centrality is highlighted in blue.
Supplementary material 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the five successive thresholds used to illustrate Figure 4: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae populations. The Highest Betweenness-centrality is highlighted in blue.
Supplementary material 4 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Comparisons among three different the individual admixture plots: Explanation note: Comparisons among the individual admixture plots of 289 individuals, for K = 3, considering correlated allele frequency, uncorrelated allele frequency, and missing data as recessive homozygotes for the null alleles, respectively.
Supplementary material 3 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 6: Explanation note: Component data are used to illustrate the structure of the subset of the Salaya5 strain and wild populations. The highest Betweenness-centrality is highlighted in blue.
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis geminata
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis geminata</em> samples were analyzed from 18 populations and 131 individuals.</p> <p>Eighteen populations were collected from South Korea, Laos, Myanmar, Thailand, and the United States.</p>
Microsatellite data on Scomber colias in NW Africa
<p><span><em><span>Scomber colias</span></em></span><span><span> is an ecologically and economically valuable species, which is targeted by industrial and artisanal fisheries throughout its geographical distribution. Some 1,169 fish were collected by trawl onboard the R.V. “Dr. Fridtjof Nansen” in the coastal waters stretching from </span></span><span>Morocco (~28°N) to Namibia (~22°S) </span><span><span>and genotyped at a suite of 8 microsatellite loci. None of the statistical procedures utilized managed to detect any significant population structure. Likewise, no marker was depicted to deviate from neutral expectations.</span></span></p> <p><span><span> </span></span><span><span>Information is available at https://imr.brage.unit.no/imr-xmlui/handle/11250/3072605</span></span><span><span> and provided in excel file called <strong><em>Scomber colias</em>_microsatellite raw data.xlx</strong>, which contains three spreadsheets:</span></span></p> <p><span><span><span>1.<span> </span></span></span></span><span><span>Geographic coordinates for each of the sampling sites that were merged into larger samples for genetic analysis.</span></span></p> <p><span><span><span>2.<span> </span></span></span></span><span><span>Raw data for microsatellite genotypes</span></span></p> <p><span><span><span>3.<span> </span></span></span></span><span><span>Microsatellites data in GenAlEx format ready for exportation in different file formats.</span></span></p>
Microsatellite data for Prosopis species sampled from different non-native populations in Kenya and Ethiopia
<p>Microsatellite data for seven loci and 711 individuals of <em>P. juliflora</em> and <em>P. pallida</em> sampled from non-native populations from Kenya and Ethiopia.</p>
The features of Tissues and Patches for "Predicting microsatellite instabilitiy from histology images with a three-level hierarchical graph fusion model"
<p>This repository contains features and corresponding coordinates of patches and tissues extracted from 430 and 326 histologic images from patients with colorectal and gastric cancers from the TCGA cohort (original whole section SVS images are freely available at https://portal.gdc.cancer.gov/). All images in this library are from formalin-fixed paraffin-embedded (FFPE) diagnostic sections (“DX” on the GDC Data Portal). This blog explains this in detail: http://www.andrewjanowczyk.com/download-tcga-digital-pathology-images-ffpe/</p> <p><strong>Preprocessing.</strong></p> <p>All SVS slices were pre-processed as follows.</p> <p>According to “Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer” these histology images were categorized into The histology images were classified as “MSS” (microsatellite stable) or “MSIMUT” (microsatellite unstable or highly mutated) according to “Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer”, which corresponds to the division of the training and test sets in the article.<br><br></p> <p>Patches were extracted at 40x objective magnification and 20x objective magnification, respectively, and the corresponding features were extracted by pre-training resnet48, respectively</p> <p>The features of Tissues are thumbnails obtained at 2.5x objective magnification and further extracted by MedSAM after extracting the masks of the tissues.</p>
Cell features for "Datasets for "Predicting microsatellite instabilitiy from histology images with a three-level hierarchical graph fusion model""
<p>This repository contains features and corresponding coordinates of cells extracted from 430 and 326 histologic images from patients with colorectal and gastric cancers from the TCGA cohort (original whole section SVS images are freely available at https://portal.gdc.cancer.gov/). All images in this library are from formalin-fixed paraffin-embedded (FFPE) diagnostic sections (“DX” on the GDC Data Portal). This blog explains this in detail: http://www.andrewjanowczyk.com/download-tcga-digital-pathology-images-ffpe/</p> <p><strong>Preprocessing.</strong></p> <p>All SVS slices were pre-processed as follows.</p> <p>According to “Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer” these histology images were categorized into “MSS” (microsatellite stable) or “MSIMUT” (microsatellite unstable or highly mutated) and corresponded to the article dividing the training and test sets.<br><br></p> <p>The features of all cells were extracted by Hovernet and Transnuseg at 40x objective magnification for extraction masking and further feature extraction</p>
Primers designed for red deer microsatellite loci
<p>Primers designed for microsatellite loci in the red deer genome</p>
Microsatellite loci in the red deer genome
<p>Position of microsatellite motifs in the red deer genome. </p>
Genotype data of 14 nuclear microsatellite loci for 18 Quercus chenii populations in China
<p>This dataset includes genotype data of 14 nuclear microsatellite loci for 419 individuals of Quercus chenii from 18 natural populations in China.</p>
Microsatellites Explorer DuckDB database
<p>This file supports the microsatellites explorer web application. It serves as a schema and data file for duckdb which was used as the in process data layer for the flask backend</p>
FIGURE 1. STRUCTURE analysis using microsatellite data shows that Sphagnum incundum form a separate genetic group from S. subnitens and S in Sphagnum incundum a new species in Sphagnum subg. Acutifolia (Sphagnaceae) from boreal and arctic regions of North America
FIGURE 1. STRUCTURE analysis using microsatellite data shows that Sphagnum incundum form a separate genetic group from S. subnitens and S. subfulvum. Sphagnum flavicomans seems to be a mixture of the recognized genetic groups. The upper panel shows data separated in two genetic groups, the middel panel shows the data separated in three genetic groups, and the lower one show the data separated in four genetic groups.
Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers
The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.
Data from: Stabilising selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci
The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor (oxtr) have evolutionarily conserved roles in vertebrate social and sexual behavior. Allelic variation at a microsatellite locus in the 5' regulatory region of these genes is associated with fitness in the bank vole Myodes glareolus. Given the low frequency of long and short alleles at these microsatellite loci in wild bank voles, we used breeding trials to determine whether selection acts against long and short alleles. Female bank voles with intermediate length avpr1a alleles had the highest probability of breeding, while male voles whose avpr1a alleles were very different in length had reduced probability of breeding. Moreover, there was a significant interaction between male and female oxtr genotypes, where potential breeding pairs with dissimilar length alleles had reduced probability of breeding. These data show how genetic variation at microsatellite loci associated with avpr1a and oxtr is associated with fitness, and highlight complex patterns of selection at these loci. More widely, these data show how stabilising selection might act on allele length frequency distributions at gene-associated microsatellite loci.
Data from: Microsatellite evidence for obligate autogamy, but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)
Although high levels of self-fertilization (>85%) are not uncommon in nature, organisms reproducing entirely through selfing are extremely rare. Predominant selfers are expected to have low genetic diversity because genetic variation is distributed among rather than within lineages, and is readily lost through genetic drift. We examined genetic diversity at 22 microsatellite loci in 105 individuals from a population of the semelparous herb Lobelia inflata L., and found (1) no evidence of heterozygosity through outcrossing, yet (2) high rates of genetic polymorphism (2-4 alleles per locus). Furthermore, this genetic variation among lineages was associated with phenotypic traits (e.g. flower colour, size at first flower). Coupled with previous work characterizing the fitness consequences of reproductive timing, our results suggest that temporal genotype-by-environment interaction may maintain genetic variation and, because genetic variation occurs only among lineages, this simple system offers a unique opportunity for future tests of this mechanism.
Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.
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.