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20 results for “population ancestry”
The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
<p class="western"><span>Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. </span></p> <p class="western"><span>The recent analysis of replicate populations from two different </span><span><i>Drosophila simulans</i></span><span> founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. </span></p> <p class="western"><span>Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.</span></p> <p class="western"> </p>
The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
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Data from: Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations
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Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population
<p>Interest in the genetic basis of variation in skin pigmentation in Native American populations led us to seek indigenous populations of the Western Hemisphere with African and minimal European admixture to study the effect of Native American ancestry on skin color. Admixture analysis from DNA collected from 458 individuals in the Kalinago territory of the Commonwealth of Dominica showed shared ancestry with East Asians at K=3 and 55% Native American, 32% African, and 11% European ancestry at K=6, the highest Native American ancestry of Caribbean populations. Skin pigmentation was 20 to 80 melanin units, averaging 46. Three albino individuals were homozygous for multi-nucleotide polymorphism OCA2<sup>NW273KV</sup> of African origin, whose population allele frequency was 0.03 and single allele effect size was -8 melanin units. Hypopigmenting allele frequencies for SLC24A5<sup>A111T</sup> and SLC45A2<sup>L374F</sup> were 0.14 and 0.05, whose single allele effect sizes were -6 and -3, respectively. Skin color plots of individuals lacking known hypopigmenting alleles suggests that Native American Ancestry reduced pigmentation by more than 20 melanin units (low and high estimates 21.8 and 28.5). Shared ancestry with East Asians at K=3 suggests potential sharing of one or more pigmentation alleles.</p>
Data from: Optimizing genomic selection for blight resistance in American chestnut backcross populations: a tradeoff with American chestnut ancestry implies resistance is polygenic
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Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population
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Data from: Analysis of iris surface features in populations of diverse ancestry
There are many textural elements that can be found in the human eye, including Fuchs' crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs' crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs' crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest.
Data from: Genetic ancestry and population differences in levels of inflammatory cytokines in women: role for evolutionary selection and environmental factors
Background: Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes. However, the impact of those genetic variations on human immunity remains understudied, especially within the context of modern lifestyles and living environments, which are drastically different from early humans in sub Saharan Africa. There are few data on population differences in constitutional immune environment, where genetic ancestry and environment are likely two primary sources of variation. Methods and Findings: In a study integrating genetic, molecular and epidemiological data, we examined population differences in plasma levels of 14 cytokines involved in innate and adaptive immunity, including those implicated in chronic inflammation, and possible contributing factors to such differences, in 914 AA and 855 EA women. We observed significant differences in 7 cytokines, including higher plasma levels of CCL2, CCL11, IL4 and IL10 in EAs and higher levels of IL1RA and IFNα2 in AAs. Analyses of a wide range of demographic and lifestyle factors showed significant impact, with age, education level, obesity, smoking, and alcohol intake, accounting for some, but not all, observed population differences for the cytokines examined. Levels of two pro-inflammatory chemokines, CCL2 and CCL11, were strongly associated with percent of African ancestry among AAs. The signal was pinpointed through admixture mapping to local ancestry at 1q23, with fine-mapping analysis refined to the Duffy-null allele of rs2814778. In AA women, this variant was a major determinant of systemic levels of CCL2 (p=1.1e-58) and CCL11 (p=2.2e-110), accounting for 19% and 40% of the phenotypic variance, respectively. Conclusion: Our data reveal strong ancestral footprints in inflammatory chemokine regulation. The Duffy-null allele may indicate a loss of the buffering function for chemokine levels. The substantial immune differences by ancestry may have broad implications to health disparities between AA and EA populations.
Data from: Analysis of iris surface features in populations of diverse ancestry
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Data from: Genetic ancestry and population differences in levels of inflammatory cytokines in women: role for evolutionary selection and environmental factors
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Prediction and Characterization of Genetically-Regulated Expression of Asthma Tissues from African-Ancestry Populations
GEO Series GSE301390. Homo sapiens. 260 samples. Type: Expression profiling by high throughput sequencing.
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
GEO Series GSE136566. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genetic ancestry and natural selection drive population differences in immune responses to pathogens in humans
GEO Series GSE81046. Homo sapiens. 503 samples. Type: Expression profiling by high throughput sequencing.
The genetic ancestry of modern Indus Valley populations from Northwest India
GEO Series GSE119653. Homo sapiens. 45 samples. Type: SNP genotyping by SNP array.
Chronic Lymphocytic Leukemia in African Ancestry Population is Characterized by Increased Genomic Instability
GEO Series GSE246521. Homo sapiens. 350 samples. Type: Expression profiling by high throughput sequencing.
Immune Gene Diversity and STING1 Variants in Shaping Cancer Immunity Across Different Genetic Ancestry Populations
GEO Series GSE314074. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World
GEO Series GSE29851. Homo sapiens. 47 samples. Type: SNP genotyping by SNP array.
Development of Polygenic Risk Scores in Colon Cancer Patients Through the Study of Ancestry and Diversity in Genetic Maps of the Brazilian Population - ORIGEM Project
ClinicalTrials.gov study NCT06917794. IPD Sharing: NO. Countries: 1. Publications: 0.
Transcriptome Diversity Associated with Ancestry and Diet in Ethnically Diverse East African Populations
GEO Series GSE99719. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Population structure and ancestry of Qinchuan cattle by GeneSeek HD Bovine 77k Genotyping BeadChip
GEO Series GSE100038. Bos taurus. 288 samples. Type: Genome variation profiling by genome tiling array; Genome variation profiling by array.
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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.