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Dataset results
244 results for “genomic variants”
A Human Induced Pluripotent Stem Cell Array-Based Genome Wide Association Study Identifies Virus Susceptibility Locus and Variants
GEO Series GSE182376. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
GEO Series GSE167479. Triticum aestivum. 204 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions (ChIP-seq)
GEO Series GSE104347. Toxoplasma gondii RH. 23 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
GEO Series GSE189158. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry
<p>(P0652) Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry</p> <p>Genotyping-by-sequencing (GBS) approaches have enabled routine high-density genome-wide DNA variant discovery in numerous agriculturally important species. Applications of GBS in octoploid (2n = 8x = 56) strawberry (Fragaria × ananassa) have been hindered by the absence of a reference genome for physically mapping DNA sequences; for discovering variants with sub-genome resolution, or effectively distinguishing homologous from homeologous variation. High-quality reference genome assemblies have recently emerged, supplying the foundation for this study, which focused on demonstrating the utility of GBS for calling sub-genome specific DNA variants in octoploid strawberry. To reduce genomic DNA complexity, double-digest protocols were tested on diverse accessions with two restriction enzyme combinations (PstI-MseI and HindIII-MseI). GBS libraries were sequenced on an Illumina HiSeq 4000 using a 150 bp paired-end protocol. For the purpose of this study, we describe the deployment of a flexible bioinformatic pipeline for GBS-facilitated variant discovery in octoploid strawberry. The percentage of uniquely mapped reads ranged from 51.41% for PstI-MseI to 55.56% for HindIII- MseI resulting in 1,591,764 and 2,362,556 unique locations, respectively. The number of discovered variants was 2.5-fold greater for HindIII-MseI (491,811) than PstI-MseI (199,486). The GBS protocols uncovered a dense genome-wide landscape of DNA variants for high- precision genetic mapping, identification of DNA variants associated with agriculturally important phenotypes, genomic-enabled breeding, and other applications in octoploid strawberry.</p> <p>Poster: PDF of poster and abstract for PAG 2018 (P0652)</p> <p>Figures: PNGs of figures on the poster</p> <p>Scrips: Txt files of SLURM scripts used to generate the follow .vcf files.</p> <p>- 8x_GBS_0_index: Uses BWA to index the reference genome (Edger et al 2019) for later use.</p> <p>- 8x_GBS_1_Demultiplex: Used Sabre to demultiplex fastq.gz files. Demultiplex_key_PE links individuals to their unique barcode.</p> <p>- 8x_GBS_2_Main: adapter removal, sequence alignment, and individual variant calling as a SLURM array. results in a .gvcf file for individuals.</p> <p>- 8x_GBS_3_Variant: population-level variant calling to a final .vcf file</p> <p>VCF: Two VCF files from the two enzyme experiments. H = HindIII-MseI; P = PstI-MseI</p>
Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate
Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted p= 2.2 x 10-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profile and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assembly. GWAS was conducted in the 942 inbred panel using both the SNP and expression data values to map sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, GWAS results for SCMV resistance using expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when using the B73 reference that contains the gene, but not when using the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated using three different reference genomes.
Identifying Genome Variants in Non-Obstructive Azoospermia (NOA) or Primary Ovarian Insufficiency (POI)
ClinicalTrials.gov study NCT07357701. IPD Sharing: NO. Countries: 1. Publications: 0.
Transcriptomic Approach for the Identification and Prioritization of Genome Variants in Neurodevelopmental Disorders With Malformation
ClinicalTrials.gov study NCT06762678. IPD Sharing: UNDECIDED. Countries: 0. Publications: 0.
H2A.X native ChIP-Seq in ESC and iPSC: Histone Variant H2A.X Mediated Epigenetic Mechanisms are Critical for Maintaining Genome Stability and Pluripotency in ES and iPS Cells
GEO Series GSE42306. Mus musculus. 33 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell genomics improves the discovery of risk variants and genes of Atrial Fibrillation [scATAC-seq]
GEO Series GSE224996. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
Open the record for dataset details and reuse information.
Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate
Open the record for dataset details and reuse information.
Genome-wide analysis of stress-responsive genes and alternative splice variants in Arabidopsis roots under osmotic stresses
GEO Series GSE229217. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Histone variant, H2B.Z demarcates the AT-rich promoter regions of the Plasmodium falciparum genome
GEO Series GSE39702. Plasmodium falciparum 3D7. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach
GEO Series GSE7761. Homo sapiens. 176 samples. Type: Expression profiling by array.
A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [plasmid DNA-seq]
GEO Series GSE263336. Homo sapiens. 4 samples. Type: Other.
Single-cell genomics improves the discovery of risk variants and genes of Atrial Fibrillation [snRNA-seq]
GEO Series GSE224995. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H33]
GEO Series GSE81862. Danio rerio. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Distinct factors control histone variant H3.3 localization at specific genomic regions
GEO Series GSE16893. Mus musculus. 38 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
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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.