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91
datasets available to search
ShareScore release 0.9.0
Dataset results
91 results for “variant identification”
Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis [MPRA]
GEO Series GSE232337. Homo sapiens. 29 samples. Type: Other.
New strategies for the identification of intronic variants related to splicing events in pancreas cancer [RNA-Seq]
GEO Series GSE228844. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify
GEO Series GSE108140. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Gene profiling-based phenotyping for identification of cellular parameters that contribute to fitness, stress-tolerance and virulence of Listeria monocytogenes variants
GEO Series GSE114672. Listeria monocytogenes; Listeria monocytogenes LO28. 10 samples. Type: Expression profiling by array.
Massively parallel identification of cis-regulatory variants in yeast promoters - Annotation runs
GEO Series GSE155942. Escherichia coli. 2 samples. Type: Other.
Identification of Three New Rugose Small Colony Variants from a Pseudomonas aeruginosa Biofilm
GEO Series GSE293895. Pseudomonas aeruginosa. 9 samples. Type: Expression profiling by high throughput sequencing.
Identification of functional variant enhancers associated with atrial fibrillation
GEO Series GSE133802. Homo sapiens. 8 samples. Type: Other.
Identification of Copy Number Variants in Patients with Hypoplastic Left Heart Syndrome and Other Congenital Heart Defects
GEO Series GSE66032. Homo sapiens. 70 samples. Type: Genome variation profiling by SNP array.
Identification of copy number variants in horses
GEO Series GSE32702. Equus caballus. 18 samples. Type: Genome variation profiling by array.
Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (CGH ZV81M)
GEO Series GSE28276. Danio rerio. 7 samples. Type: Genome variation profiling by genome tiling array.
New strategies for the identification of intronic variants related to splicing events in pancreas cancer
GEO Series GSE229007. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing.
Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [RNA-seq]
GEO Series GSE80741. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array)
GEO Series GSE28239. Danio rerio. 7 samples. Type: Expression profiling by array.
Identification of genetic variants that affect histone modifications in human cells
GEO Series GSE47991. Homo sapiens. 50 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients
GEO Series GSE185795. Homo sapiens; other sequences. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
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.
Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic proxy for EPO-increasing therapies.
<p>Summary statistics for the genome-wide association study meta-analysis of circulating EPO in 6,127 individuals of European and African American descent. Effect sizes are aligned to allele 1. </p> <p>Description of column names:<br> # Marker - this is the marker name; chromosome:position<br> # Allele1 - the first allele for this marker in the first file where it occurs<br> # Allele2 - the second allele for this marker in the first file where it occurs<br> # Freq1 - weighted average of frequency for allele 1 across all studies<br> # FreqSE - corresponding standard error for allele frequency estimate<br> # MinFreq - minimum frequency for allele 1 across all studies<br> # MaxFreq - maximum frequency for allele 1 across all studies<br> # Effect - overall estimated effect size for allele1<br> # StdErr - overall standard error for effect size estimate<br> # P-value - meta-analysis p-value<br> # Direction - summary of effect direction for each study, with one '+' or '-' per study. Order of the studies is InCHIANTI, BLSA, HealthABC Europeans, PREVEND, HealthABC African Americans<br> # HetISq - I^2 statistic which measures heterogeneity on scale of 0-100%<br> # HetChiSq - chi-squared statistic in simple test of heterogeneity<br> # df - degrees of freedom for heterogeneity statistic<br> # HetPVal - P-value for heterogeneity statistic<br> # TotalSampleSize - overall sample size for that variant in the meta-analysis</p> <p> </p>
Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic proxy for EPO-increasing therapies.
<p>Raw fast-qc files for RNA sequencing analysis of whole <em>EPO</em> gene knock-outs generated through CRISPR-Cas9 gene-editing in HEK-293 cells compared to wild-type controls. </p> <p>Wild-type cell-lines (Empty 1 - Empty 4) were transfected with empty CRISPR-Cas9 constructs to ensure cells were treated under the same experimental conditions. Whole EPO gene knock-outs were generated using a double gRNA approach with CRISPR-Cas9 gene-targeting. Two whole EPO gene knock-out cell-lines were generated (KO-A and KO-B).</p> <p>Library preparation was performed using the TruSeq DNA HT Library Preparation Kit using the 3’ poly-A tail primer Oligo(dT) from Illumina (Illumina, California, USA). RNA Sequencing was performed using the Illumina HiSeq 2500 high-throughput sequencing system (Illumina, California, USA). We resulted in 75 bp paired-end sequences.</p> <p> </p>
The BRAVE Study- The Identification of Genetic Variants Associated With Bicuspid Aortic Valve Using a Combination of Case-control and Family-based Approaches.
ClinicalTrials.gov study NCT04514445. IPD Sharing: NO. Countries: 1. Publications: 0.
Identification of the Genetic Variants Responsible for Primary Biliary Cirrhosis (PBC)
ClinicalTrials.gov study NCT00145964. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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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.