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.
927
datasets available to search
ShareScore release 0.9.0
Dataset results
927 results for “genetic study”
LA1141 × OH8245 inbred backcross (IBC) single nucleotide polymorphism (SNP) markers for genetic studies
<p>The LA1141 × OH8245 157 polymorphic SNP markers from an optimized tomato panel Sim et al., 2012 were used for linkage map construction in the BC<sub>2</sub>S<sub>3</sub> IBC and composite interval mapping QTL analysis. Genetic map position and physical position corresponding to Sl4.0 (Hosmani et al., 2019), and flanking sequences are provided.</p>
Processed data for the study on "Chromatin 3D interactions mediate genetic effects on gene expression"
<p>This repository contains the processed data that was generated as part of the following study:</p> <p>Delaneau et al. (2019) <strong>Chromatin 3D interactions mediate genetic effects on gene expression.</strong></p> <p><em>Abstract:</em> Studying the genetic basis of gene expression and chromatin organization is key to characterize the effect of genetic variability on the function and structure of the human genome. Here, we unravel how genetic variation perturbs gene regulation using a dataset combining activity of regulatory elements, gene expression and genetic variants across 317 individuals and two cell types. We show that variability in regulatory activity is structured at the intra- and inter-chromosomal levels within 12,583 Cis Regulatory Domains and 30 Trans Regulatory Hubs that highly reflect the local (i.e. Topologically Associating Domains) and global (i.e. open/close chromatin compartments) nuclear chromatin organization. These structures delimit cell type specific regulatory networks that control gene expression/co-expression and mediate the genetic effects of <em>cis</em>- and <em>trans</em>-acting regulatory variants on genes.</p> <p> </p> <p>This repository contains:</p> <ol> <li>Chromatin QTLs for H3K27ac, H3K4me1 and H3K4me3 discovered in 317 Lymphoblastoids Cell Lines (LCLs) and 78 Fibroblasts.</li> <li>Molecular QTLs affecting the activity and structure of Cis Regulatory Domains (CRDs) in LCLs.</li> <li>Basic information about the full set of genetic variants being analyzed in the study.</li> <li>The peak coordinates, their hierarchy based on inter-individual correlation and the CRD calls for both LCLs and Fibroblasts.</li> <li>The functional links discovered in LCLs between CRDs and genes.</li> <li>eQTLs for LCLs.</li> <li>A README file containing the description of the file format for each file.</li> </ol>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </p>
A scalable, accurate, and universal analysis framework using individual-level allele frequency for large-scale genetic association studies in an admixed population
<p>Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in Caucasian population. Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including binary trait, quantitative trait, time-to-event trait, longitudinal traits, etc. For each genetic variant, SPAmix uses genotype data and genetic principal components (PCs) to estimate individual-level allele frequency, which is subsequently used to calibrate p values via a retrospective analysis. A hybrid strategy including saddlepoint approximation (SPA) can greatly increase the accuracy to analyze rare genetic variants, especially if the phenotypic distribution is unbalanced or extremely unbalanced. Compared to Tractor, SPAmix does not require local ancestry information and can be straightforwardly applicable to a multi-way admixed population. Meanwhile, SPAmix can also be extended to SPAmix<sub>local</sub> in which the local ancestry can be incorporated if available. In addition, we propose SPAmix<sub>CCT</sub> to combine the p values of SPAmix and SPAmix<sub>local</sub> via Cauchy combination (CCT). SPAmix<sub>local</sub> performs close to Tractor when analyzing quantitative traits and is more accurate when analyzing binary traits with an unbalanced case-control ratio. And SPAmix<sub>CCT </sub>is an optimal unified approach for various cross-ancestry genetic architectures. Extensive simulation studies and real data analyses of 369,314 UK Biobank individuals from multiple ancestries demonstrated that SPAmix is scalable and can discover novel hits while controlling type I error rates well.</p>
Figure 1 in Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region - Greece
Figure 1. The study area in Kastoria region and capture locations (red dots) for the 75 living bears.
Georeferenced data for the study Environmental suitability throughout the late Quaternary explains population genetic diversity
<p>Data filtered from GBIF (datasetKey: 50c9509d-22c7-4a22-a47d-8c48425ef4a7) Contains 150 records of the <i>Sciurus aberti </i>squirrel filtered in latitudinal windows of 5 degrees from 20 to 45 degrees N. </p>
Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits
<p>This (zipped) folder contains 3 sub-folders:</p> <p>#**********************************************************************************************************<br>The "bin" folder contains fuctions and gentic maps needed for analyes<br>bin \<br> predLink.R - function to predict linkage <br> sibREML_v0.1.1.R - function to run SibREML<br> sim-sib-array.R - script to simulate sib-pairs from parental haplotypes<br> Summarised_genetic_map_bcf.txt - genetic map per 0.5-cM long segments, based on map from bcftools <br> (BCFtools: https://samtools.github.io/bcftools/bcftools.html)<br> Summarised_genetic_map_OMNI.txt - genetic map per 0.5-cM long segments, based on OMNI map <br> (https://github.com/joepickrell/1000-genomes-genetic-maps/tree/master/interpolated_OMNI)<br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "SIM" folder contains the simulation pipeline (scripts 01-15) as well as IBD sharing and simulated phenotypes for Simulated sib-pairs.<br>SIM \<br> 01_sim-sib-array.sh *pre-run*<br> 02_bed_recode_bcf_map.sh *pre-run*<br> 03_make_merlin.R *pre-run*<br> 04_error_merlin.sh *pre-run*<br> 05_merlin_IBD.sh *pre-run*<br> 06_sample_causal_snps.R *pre-run*<br> 07_simulate_pheno.sh *pre-run*<br> 08_bhat_gwas.R *can be run using provided data* <br> 09_Linkage_VH.R *can be run using provided data* <br> 10_predLink.R *can be run using provided data*<br> 11_phi_hat.R *can be run using provided data*<br> 12_IBD_Mb.R *can be run using provided data*<br> 13_IBD_cM_recombrate_stratified.R *can be run using provided data*<br> 14_SibREML.R *can be run using provided data*<br> 15_SibREML_stratified_Q4.R *can be run using provided data*<br> causal_snps \ *provided causal SNPs*<br> IBD_results \ *provided IBD-probabilities for 1000 simulated sib-pairs*<br> Linkage_VH_results \ <br> pheno \ *provided simulated phenotypes (h2=1) for 8 genetic architectures*<br> Phi_hat_results.txt<br> predicted \<br> README<br> SibREML_results.txt<br> SibREML_stratified_Q4.txt</p> <p>The data can be used to run Linkage analysis, predict linkage, estimate phi_hat, <br>as well as estimate non-stratified and recombination rate stratified sib-heritability (h2_FS and c).<br>The README is provided within the folder. <br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "HT_BMI" folder contains data and scripts to predict linkage and estimate phi_hat for height and BMI.<br>HT_BMI \<br> 01_predLink_HT_BMI.R<br> 02_phi_hat_HT_BMI.R<br> gws_sumstats \ *provided summary GWAS summary statistics to predict linkage for height and BMI*<br> Linkage_results \ *provided linkage meta-analysis results for height and BMI from this study*<br> Phi_hat_results_HT_BMI.txt<br> PREDLINK_bmi.txt<br> PREDLINK_height.txt<br> README<br>The README is provided within the folder.<br>#**********************************************************************************************************</p> <p><strong> </strong></p>
F I G U R E 5 Phylogenetic study using the 5S in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 5 Phylogenetic study using the 5S rDNA sequences from Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper
Summary statistics from "Genetic Association Study of Eight Steroid Hormones and Implications for Sexual Dimorphism of Coronary Artery Disease"
<p>GWAMA summary statistics of four steroid hormone levels using fixed-effect model and GWAS summary statistics of four other steroid hormones.</p> <p>When using this data, please cite: Pott J, Bae YJ, Horn K, et al.. Genetic Association Study of Eight Steroid Hormones and Implications for Sexual Dimorphism of Coronary Artery Disease. <em>J Clin Endocrinol Metab</em> <strong>2019</strong> Nov 1;104(11):5008-5023. doi: 10.1210/jc.2019-00757</p> <p>All txt files contain the following columns:</p> <ul> <li>markername</li> <li>chr</li> <li>bp_hg19 (base position according to hg19)</li> <li>effect_allele</li> <li>other_allele</li> <li>effect_allele_freq</li> <li>min_info (minimal info score across all used studies)</li> <li>n (sample size per SNP)</li> <li>beta (effect estimate)</li> <li>se (standard error)</li> <li>p (p-value)</li> <li>CochransQ (only in GWAMA; SNP heterogeneity across studies)</li> <li>pCochransQ (only in GWAMA; p-value of Cochrans Q value)</li> </ul>
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
<p><strong>PREMISE</strong>: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function.</p> <p><strong>METHODS</strong>: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass <em>Leymus chinensis</em>. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.</p> <p><strong>RESULTS</strong>: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.</p> <p><strong>CONCLUSIONS</strong>: We found strong genetic structure among patches of <em>L. chinensis</em>. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.</p>
Oenothera Section Calylophus population genetic study
<p><strong>Premise</strong>: Animal pollinators play an important role in pollen dispersal. Differences in foraging patterns, flight distances and grooming behaviors are assumed to have consequences for genetic diversity of plants but are rarely tested explicitly. Here, we assess the role of pollinator functional groups with different foraging behaviors (hawkmoth and bee) in generating patterns of genetic diversity over similar geographic ranges for two closely related taxa.</p> <p><strong>Methods</strong>: This study focuses on two members of <em>Oenothera</em> section <em>Calylophus</em> that co-occur on gypsum outcrops throughout the Chihuahua Desert but differ in floral phenotype and primary pollinator: <em>Oenothera</em> <em>gayleana</em> (bee) and <em>O</em>. <em>hartwegii</em> subsp. <em>filifolia</em> (hawkmoth). We measured breeding system and floral traits in the greenhouse and conducted a population genetic study at the local (<13km; four populations) and landscape (60–440km; five populations) scales using 10–11 nuclear (pollen dispersal) and three plastid (seed dispersal) microsatellite markers. </p> <p><strong>Key Results</strong>: Both taxa were self-incompatible and floral traits were consistent with expectations for different pollinators. We found no evidence of genetic structure at the local scale, but at the landscape scale, <em>O</em>. <em>gayleana</em> showed greater differentiation and significant isolation by distance than <em>O</em>. <em>hartwegii</em> subsp. <em>filifolia</em>. The plastid data were consistent with gravity dispersal of seeds and suggest that pollen dispersal is the principal driver of genetic structure in both species.</p> <p><strong>Conclusions</strong>: We demonstrate that pollinator functional groups can impact genetic differentiation in different and predictable ways. Hawkmoths, with larger foraging distances, can maintain gene flow across greater spatial scales than bees.</p>
Data and codes from "Daniel et al. What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA"
<p><span>Data and codes used for </span><span>“Daniel et al. What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA”</span></p>
Figure 2 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 2. Idiograms of the accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa - PI" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D), "Cateto Roxo 99" (E), "Roxo de Minas" (F), and "Sergipe" (G). Yellow dash and circle represent the CMA+/DAPI- band. Chromosomal order (CO), chromosome morphology (CM), metacentric (M), submetacentric (SM), short arm (p), and long arm (q). Vertical bar in karyogram and ideogram = 10 µm.
Figure 1. Allium sativum L in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 1. Allium sativum L.cytological data obtained by conventional Giemsa staining.Prophase and interphase nucleus (A), prometaphase (B), and metaphase (C) obtained with the use of antimitotic. Mitotic cycle is shown in d-f: anaphase (D), end of anaphase (E), and telophase (F). Dots and red arrow indicate the distended nucleolar organiser region (NOR). Bar = 10 µm.
A field study of the molecular response of brown macroalgae to heavy metal exposure: an (epi)genetic approach
<p>We used next-generation sequencing to study DNA methylation changes and DNA sequence variation (SNPs) in thalli from four populations of the brown macroalgae <em>Fucus vesiculosus</em> reciprocally transplanted between two polluted and two unpolluted sites. For this, we performed reduced representation bisulfite DNA sequencing.</p>
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).
Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies
<p>GWAS summary results from the paper</p> <p>The Lancet Respiratory Medicine: http://dx.doi.org/10.1016/S2213-2600(19)30055-4</p> <p>Preprint: https://doi.org/10.1101/427427</p>
Figure 6 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 6. Maximum likelihood (ML) tree of bufonid frogs based on nucleotide sequences of the mitochondrial 16S rRNA gene with Leptophryne borbonica as an outgroup. The bootstrap support (>50%) is indicated at nodes in the order of ML (500) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%). Specimens examined in this study are indicated by boldface type.
Figure 2 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 2. Maximum likelihood (ML) tree based on nucleotide sequences of the mitochondrial 16S rRNA gene from 88 haplotypes of frogs (Table 1), with Xenopus laevis as an outgroup. Bootstrap support (>50%) is indicated at nodes in the order of ML (1000) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%).
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
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.