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1,155 results for “loci”
Summary Statistics from "Genome-wide meta-analysis of phytosterols reveals five novel loci and a detrimental effect on coronary atherosclerosis"
<p>Summary statistics of meta GWAS of phytosterols.</p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: validation cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the validation cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include: </p> <p>(1) SNP genotypes for the two SNPs which overlap with the discovery cohort<br> - (nicaragua_snp_genotypes_ints.tsv) -- SNP genotypes as integers<br> - (nicaragua_snp_genotypes_strings.tsv) -- SNP genotypes as allele strings <br> (2) the ancestry PCs for each individual in the validation cohort (nicaragua_snp_ancestry_PCA.tsv)<br> (3) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (4) a file including IMGT genes used for parsing TCRA repertoire data (human_vj_alleles_alpha.tsv)<br> (5) Parsed TCRA repertoire data (nicaragua_parsed_TCRA.tgz)<br> (6) Parsed TCRB repertoire data (nicaragua_parsed_TCRB.tgz) </p> <p><strong>Corresponding raw validation cohort TCR repertoire data is available here:</strong> https://www. ncbi.nlm.nih.gov/bioproject/PRJNA762269 (The BioProject database, accession number: PRJNA762269)</p> <p><strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci
<p>Trans-ethnic meta-analysis results for eGFR EWAS</p> <p>Description of variables:</p> <p>CpG CPG name<br> chr Chromosome <br> pos_hg38 Position hg38 <br> Beta Effect <br> SE Standard error <br> P P value <br> totalsamplesize number of participants <br> direction direction of effect for studies <br> hetpval P value for heterogeneity <br> hetdf Degree of freedom <br> gene Gene location</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a zenodo DOI generated for you go to ewascatalog.org/upload. </p>
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
<p><span>Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, <em>MATA </em>and <em>MATB</em>. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus <em>Trichaptum </em>(Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three <em>Trichaptum </em>species. We characterized the chromosomal location of <em>MATA </em>and <em>MATB</em>, the molecular structure of <em>MAT </em>regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple <em>MAT </em>alleles segregating before the speciation event of <em>Trichaptum </em>species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. <em>In vitro </em>crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in <em>Trichaptum </em>is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.</span></p>
Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 970 Pedunculate oak trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. The data set includes the sample IDs, geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism).</p>
Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci
<p>Understanding the genetic aetiology of loci associated with disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarise the conservation of genomic (exonic and multi-cell regulatory) features and complex disease associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.</p>
Quantitative trait loci mapping in cichlid fishes: Aulonocara koningsi x Metriaclima mbenjii and Labidochromis caeruleus x Labeotropheus trewavasae
<p>Since the time of Darwin, biologists have sought to understand the evolution and origins of phenotypic variation. To understand the genetic and molecular sources of morphological differences, we capitalize on the cichlid fish system. Cichlids of the East African Rift Lakes have undergone an extensive adaptive radiation, including variation in body shape, head shape, and pigmentation. These morphological differences are often intimately linked to the ecology and behavior of these animals. Here, we investigate the genetic basis of these phenotypes using quantitative trait loci (QTL) mapping using four genera of Lake Malawi cichlids and two F<sub>2</sub> hybrid populations. The first hybrid cross is between <em>Aulonocara koningsi</em>, which lives in the open sandy region and feeds insects from the open sand, and <em>Metriaclima mbenjii</em>, an omnivore rock-dwelling fish. The second cross is between <em>Labidochromis caeruleus</em>, a suction-feeding insectivore that swims continuously searching for prey, and <em>Labeotropheus trewavasae</em>, which feeds by biting or scraping attached algae from the rocks in its benthic habitat. Such work can provide insights into the molecular basis of phenotypic adaptation, the genetic architecture of morphology, and the evolution of cichlid fishes.</p>
Evolution of physical linkage between loci: simulations output
<p>Coupling of multiple barriers to gene-flow, such as divergent local adaptation and reproductive isolation, facilitates speciation. However, alleles at loci that contribute to barrier effects can be dissociated by recombination. Models of linkage between diverging alleles often consider elements that reduce recombination, such as chromosomal inversions and alleles that modify recombination rate between existing loci. In contrast, here we consider the evolution of linkage due to close proximity of loci on the same chromosome. Examples of such physical linkage exist in several species, but in other cases strong associations are maintained without physical linkage. We use an individual-based model to study the conditions under which physical linkage between loci controlling ecological traits and mating preferences might be expected to evolve. We modelled a single locus controlling an ecological trait that acts also as a mating cue<span>.</span> Mating preferences are controlled by multiple loci, formed by mutations that are randomly placed in the "genome", within varying distances from the ecological trait locus, allowing us to examine which genomic architectures spread across the population. </p>
Data and code from "Temporal allele frequency changes in large-effect loci reveal potential fishing impacts on salmon life-history diversity" (Miettinen et al. 2024)
<p>This archive contains code and data files to perform analyses detailed in Miettinen et al. (2024, Evolutionary Applications, https://doi.org/10.1111/eva.13690).</p>
Example coverage files of TCRA/TCRB/TCRG/IGH loci
<p>WGS coverage files for the TCRA/TCRB/TCRG and IGH loci to be used as test data</p>
Code from: Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation
<p>Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, <em>six6</em> and <em>vgll3</em>, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in the <em>vgll3</em>, but with early maturation in the <em>six6</em> locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the <em>six6 </em>locus, and by both parents' genotypes in the <em>vgll3</em> locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.</p>
Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci
<p>Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.</p>
Data from: Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)
<p>Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (<em>Anastraphia</em>, <em>Cnicothamnus</em>, <em>Cyclolepis</em>, <em>Gochnatia</em>, <em>Moquiniastrum</em>, <em>Nahuatlea</em>, <em>Pentaphorus</em>, <em>Richterago</em>, <em>Tehuasca</em>). One recently described genus, <em>Vickia</em>, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific <em>Cyclolepis</em>, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as <em>incertae sedis</em> since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic <em>Moquiniastrum</em> with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for <em>Cyclolepis</em> and <em>Richterago</em>, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of <em>Moquiniastrum</em> corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in <em>Moquiniastrum</em> and <em>Richterago</em>), dimorphic and subdimorphic corollas (in <em>Cnicothamnus</em>, <em>Moquiniastrum</em>, and <em>Richterago</em>), and the presence of marginal female corollas (in <em>Moquiniastrum</em> and <em>Richterago</em>). Within <em>Moquiniastrum</em>, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.</p>
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>
Association mapping identified novel candidate loci affecting wood formation in Norway spruce
<p>Genotypic data set for the association mapping in Norway spruce for wood formation and tracheid traits.</p>
PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity
<p><strong>Introduction</strong></p> <p>These are the <em>Summary Level-data</em> as presented in:</p> <p>"PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity". <em>Nature Communications </em>volume 9, Article number: 2904 (2018) doi: 10.1038/s41467-018-04766-9 </p> <p>If you use these data please cite the corresponding manuscript, which can be downloaded here: https://www.nature.com/articles/s41467-018-04766-9. When you have any questions or comments regarding this study or these files, please contact me via:</p> <p>Jessica van Setten, PhD | <em>Department of Cardiology, University Medical Center Utrecht, Utrecht University</em> | j.vansetten [at] umcutrecht [dot] nl</p> <p> </p> <p><strong>Files and description</strong></p> <p>The file PR_interval_July2018_summary_results.txt is gzipped and contains the PR interval GWAS meta-analysis summary results of 92,000 European samples. The imputation reference panel used for most studies was HapMap2 (please note: hg18, build36). </p> <ul> <li><em>SNP</em> - variantID (rsID).</li> <li><em>CHR</em> - chromosome numbers [1-22 and X].</li> <li><em>POS</em> - base pair position, hg18 / build36.</li> <li><em>CODED_ALLELE</em> - coded allele, <em>i.e.</em> the effect allele, as represented (and harmonized) across cohorts. Note that this is not necessarily the minor allele.</li> <li><em>NON_CODED_ALLELE</em> - the other allele, <em>i.e.</em> the non-effect allele.</li> <li><em>CODED_ALLELE_FREQ</em> - coded allele frequency, <em>i.e.</em> the effect allele frequency. Note that this is not necessarily the minor allele frequency.</li> <li><em>BETA_FIXED</em> - beta from the fixed-effects model.</li> <li><em>SE_FIXED </em>- standard error from the fixed-effects model.</li> <li><em>P_FIXED </em>- P-value from the fixed-effects model.</li> </ul>
Constant Hue Loci Data - Hung and Berns (1995)
<p>This deposit only contains the extracted tabular data from <em>Hung, P.-C., & Berns, R. S. (1995). Determination of constant Hue Loci for a CRT gamut and their predictions using color appearance spaces. Color Research & Application, 20(5), 285–295. doi:10.1002/col.5080200506</em>, please use the following link or DOI for the original publication.<br> <br> <strong>Source URL</strong>: <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/col.5080200506">https://onlinelibrary.wiley.com/doi/abs/10.1002/col.5080200506</a><br> <strong>Source DOI</strong>: 10.1002/col.5080200506f</p> <p><strong>Determination of constant Hue Loci for a CRT gamut and their predictions using color appearance spaces</strong></p> <p>A colorimetrically characterized computer‐controlled CRT display was used to determine 24 loci of constant perceived hue for pseudo‐object related stimuli, sampling the display's interior color gamut at constant lightness and the edge of its gamut at variable lightness. Nine observers performed three replications generating matching data at 132 positions. the constant hue loci were used to evaluate the correlation between perceived hue and hue angle of CIELAB, CIELUV, Hunt, and Nayatani color appearance spaces. the CIELAB, CIELUV, and Hunt spaces exhibited large errors in the region of the blue CRT primary, while the Nayatani and CIELUV spaces produced large errors in the region of the red primary for constant lightness stimuli. Along the edge of the CRT's color gamut (variable lightness stimuli), all the spaces had a similar trend, large errors in the cyan region. the differences in performance between the four spaces were not statistically significant for the constant lightness stimuli. For the variable lightness stimuli, CIELAB and CIELUV had statistically superior performance in comparison with the Nayatani space and equal performance in comparison with the Hunt space. It was concluded that for imaging applications, a new color appearance space needs to be developed that will produce small hue error artifacts when used for gamut mapping along loci of constant hue angle.</p>
Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control
<p>Summary statistics for trans-ancestral analysis presented in "Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control" by Boocock et al.</p> <p>Columns in order with descriptions are:</p> <p>SNP(rsid) CHROM POS(genome position) REF(reference allele) ALT(alternative allele) Z_EUR(zscore european) Z_EAS(zscore east asian) P_META(p-value from trans-ancestral meta-analysis) </p>
Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen (genome assembly, annotation dataset, core- and pan-genome loci)
<p>This dataset refers to the analysis of 49 <em>Arcobacter butzleri</em> genomes and includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files), the respective amino acid sequences of the translated CDS sequences (.faa files), the nucleotide alignments of all the 1165 core-genome loci, the nucleotide alignments of the genes <em>hecA</em>, <em>tetR </em>and <em>porA</em>, the categorized amino acid sequences of the six hypervariable regions of PorA, and the nucleotide sequences of the first allele of each of the 7474 pan-genome loci with the respective complete allelic profile matrix.</p> <p>All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441).</p>
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.