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183 results for “association mapping”
Multi-reference genome and K-mer based association mapping in Zymoseptoria tritici
<p>Data tables for a study of multi-reference genome and K-mer based association mapping of the fungal wheat pathogen <em>Zymoseptoria tritici</em></p>
MAP 4 in Systematics And Analysis Of The Radiation Of Orthotylini Plant Bugs Associated With Callitroid Conifers In Australia: Description Of Five New Genera And 32 New Species (Heteroptera: Miridae: Orthotylinae)
MAP 4. Distribution of Erysivena species.
MAP 3 in Systematics And Analysis Of The Radiation Of Orthotylini Plant Bugs Associated With Callitroid Conifers In Australia: Description Of Five New Genera And 32 New Species (Heteroptera: Miridae: Orthotylinae)
MAP 3. Distribution of Callitricola species.
MAP 5 in Systematics And Analysis Of The Radiation Of Orthotylini Plant Bugs Associated With Callitroid Conifers In Australia: Description Of Five New Genera And 32 New Species (Heteroptera: Miridae: Orthotylinae)
MAP 5. Distribution of Erysivena species.
MAP 2 in Systematics And Analysis Of The Radiation Of Orthotylini Plant Bugs Associated With Callitroid Conifers In Australia: Description Of Five New Genera And 32 New Species (Heteroptera: Miridae: Orthotylinae)
MAP 2. Distribution of Callitricola species.
MAP 1 in Systematics And Analysis Of The Radiation Of Orthotylini Plant Bugs Associated With Callitroid Conifers In Australia: Description Of Five New Genera And 32 New Species (Heteroptera: Miridae: Orthotylinae)
MAP 1. Distribution of Avititerra and Blattakeraia species.
Single-Cell Mapping Reveals Several Immune Subsets Associated with Liver Metastasis of Pancreatic Ductal Adenocarcinoma
<p>Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment.</p> <p>The details about the files uploaded are as follows:</p> <p>1. panelA_Blood.zip includes 10 .fcs files from blood samples in Panel A;</p> <p>2. panelA_LN.zip includes 5 .fcs files from lymph node samples in Panel A;</p> <p>3. panelA_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel A;</p> <p>4. panelB_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel B;</p> <p>5. panel_metadata.xlsx describes marker used in Panel A and B;</p> <p>6. sample_metadata.xlsx describes detailed sample information.</p>
Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
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Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
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Supplemental material for: Genome-wide association study and fine-mapping using imputed sequences to prioritize candidate genes for 30 complex traits in 50,309 Holstein bulls
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Ecophysiology and specialized metabolite trait data for the sunflower association mapping population
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Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)
<p><span><span>Mung bean (<i>Vigna radiata</i> L.) quality is dependent on seed chemical composition, which in turn determines the benefits of mung bean consumption for human health. While rich in a range of nutritional components, such as protein, macro- and micro- nutrients, carbohydrates and vitamins, mung bean remains less well studied than other legume crops. Mung bean genomics and genetic resources are relatively sparse. To further improve nutritional levels of mung bean grain requires genome-wide marker system tools. The objectives of this research were to develop these tools and conduct nutrient analysis in order to 1) identify single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) and to 2) perform genome-wide association studies (GWAS) for levels of calcium, iron, potassium, manganese, phosphorous, sulfur, and zinc in mung bean grain produced over two years of field experiment. A total of 112 GWAS models were explored using 6,486 high quality SNPs discovered in 92 cultivated mung bean accessions chosen from USDA core collection that represented 13 countries. The data obtained allowed for the identification of 43 associated SNPs and 20 main genomic regions that explained on average 22 % of the overall variation in seed macro- and micro- nutrients concentration on the basis of a multiple-year analysis. Most of the regions discovered in this study provide valuable candidate gene to use in future breeding of new varieties of mung bean with novel nutritional properties. Identification of the <a>underlying genes</a> will help to reveal the genetic control of mung bean seed nutritional property. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) in the species <i>V</i>. <i>radiata</i>, including wide and narrow crosses with / between cultivated and wild mung bean.</span></span></p>
Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection
Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) in wheat. It is the most important leaf blotch pathogen in Norwegian spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility have been identified. Some of these QTL are the result of underlying gene-for-gene interactions involving necrotrophic effectors (NEs) and corresponding sensitivity (Snn) genes. A collection of diverse spring wheat lines was evaluated for SNB resistance/susceptibility over seven growing seasons in the field. In addition, wheat seedlings were inoculated and infiltrated with culture filtrates (CFs) from four single spore isolates and infiltrated with semi-purified NEs (SnToxA, SnTox1 and SnTox3) under greenhouse conditions. In adult plants, the most stable SNB resistance QTL were located on 2B, 2D, 4A, 4B, 5A, 6B, 7A and 7B. The QTL on 2D was effective most years in the field. At the seedling stage, the most significant QTL after inoculation were located on 1A, 1B, 3A, 4B, 5B, 6B, 7A and 7B. The QTL on 3A and 6B were significant both after inoculation and CF infiltration, indicating the presence of novel NE-Snn interactions. The QTL on 4B and 7A were significant in both seedlings and adult plants. Correlations between SnToxA sensitivity and disease severity in the field were significant. To our knowledge, this is the first genome wide association mapping study (GWAS) to investigate SNB resistance at the adult plant stage under field conditions.
The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets
<p>High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (<em>Entosphenus tridentatus</em>) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations likely explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent datasets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.</p>
Data from: A nested association mapping panel in Arabidopsis thaliana for mapping and characterizing genetic architecture
<p><span><span><span><span><span><span><span><span><span><span><span>Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred populations (RILs) of <i>Arabidopsis thaliana</i>, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.</span></span></span></span></span></span></span></span></span></span></span></p>
Associated Motion in Tibeto-Burman: color map
<p>This is a map of languages surveyed in an article on association motion in Tibeto-Burman languages for the journal Linguistic Typology. </p>
Data from: Genetic mapping identifies a major locus spanning P450 clusters associated with pyrethroid resistance in kdr-free Anopheles arabiensis from Chad
Prevention of malaria transmission throughout much of Africa is dependent on bednets that are impregnated with pyrethroid insecticides. Anopheles arabiensis is the major malaria vector in Chad and efforts to control this vector are threatened by the emergence of pyrethroid resistance. WHO bioassays revealed that An. arabiensis from Ndjamena is resistant to pyrethroids and dichlorodiphenyltrichloroethane (DDT) but fully susceptible to carbamates and organophosphates. No 1014F or 1014S kdr alleles were detected in this population. To determine the mechanisms that are responsible for resistance, genetic crosses were established between the Ndja strain and an insecticide susceptible population from Mozambique. Resistance was inherited as an autosomal trait and quantitative trait locus (QTL) mapping identified a single major locus on chromosome 2R, which explained 24.4% of the variance in resistance. This QTL is enriched in P450 genes including 25 cytochrome P450s in total. One of these, Cyp6p4 is 22-fold upregulated in the Ndja strain compared with the susceptible. Piperonyl butoxide (PBO) synergist and biochemical assays further support a role for P450s in conferring pyrethroid resistance in this population.
Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.
Data from: Utility of pooled sequencing for association mapping in non-model organisms
High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in non-model organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) libraries showed that approximately 48% genome coverage per library could be achieved with reasonable sequencing effort. We additionally examined male and female O. tshawytscha libraries to illustrate how Pool-Seq techniques can successfully map known genes associated with functional differences among sexes such as growth hormone 2. Finally, we compared pools of individuals of different spawning ages for each sex to discover novel genes involved with age at maturity in O. tshawytscha such as opsin4 and transmembrane protein19. While not appropriate for every system, Pool-Seq data processed by the PoolParty pipeline is a practical method for identifying genes of major effect in non-model organisms when high genome coverage is necessary and cost is a limiting factor.
Data from: Association mapping of genetic risk factors for chronic wasting disease in wild deer
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.
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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)
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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.