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23
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ShareScore release 0.9.0
Dataset results
23 results for “exomic variants”
Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
<p>This dataset consists of the reference data files, metadata and processed results files for the paper "Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants," which investigates clonality in normal human dermal fibroblast cell populations in 32 cell lines from distinct donors, using bulk whole-exome sequencing and single-cell RNA-sequencing data.</p> <p>This dataset contains everything required to reproduce the results presented in the paper from processed data and results of our data processing workflows. Our analyses can be reproduced using the <a href="https://github.com/davismcc/fibroblast-clonality">source code</a> and instructions available at our <a href="https://davismcc.github.io/fibroblast-clonality/">project website</a>.</p> <p>The <em>entire</em> analysis workflow from raw data to final results is also reproducible but is substantially more complicated and computationally intensive. It also requires large datasets to be obtained from other repositories. Specifically, single-cell RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI under accession number E-MTAB-7167. Whole-exome sequencing data is available through the HipSci portal (www.hipsci.org). Combined with the dataset in this repository and following the instructions on the project website, it is possible to run our entire analysis pipeline.</p> <p> </p>
Summary statistics for "Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's Disease"
<p>These are the burden test results (summary statistics) for the publication:</p> <p>"Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s Disease",</p> <p>Nature Genetics, 2022.</p> <p> </p> <p><em>Format: tab-separated-value.</em></p> <p><em>Fields:</em></p> <ul> <li><em>gene_stable_id: Ensembl gene id</em></li> <li><em>gene_name: standard gene name</em></li> <li><em>pvalue: burden test significance (likelihood ratio test, population structure correction based on 6 PCA components)</em></li> <li><em>cmac_all: sum of minor allele dosages across all contributing samples and variants</em></li> <li><em>group: variant group (LOF, LOF+REVEL>=75, LOF+REVEL>=50, LOF+REVEL>=25, see publication methods for further selection criteria).</em></li> <li><em>beta/se: beta/se of logistic ordinal regression (see publication methods). Positive = risk-increasing. Negative = risk-decreasing.</em></li> </ul> <p> </p>
Genetic variants (chr. 6) from Old World Schistosoma mansoni exomes
<p>Variant calling file (VCF) produced from exome libraries of <em>Schistosoma mansoni</em> (bloodfluke) samples from the Old Wold (West Africa (Senegal, Niger), East Africa (Tanzania), and Middle East (Oman)). One sample form the New World (Caribbean (HR9)) was added for comparison. The variants were called on the 3 Mb of chromosome 6 centered on the <em>SmSULT-OR</em> gene. This gene is involved in resistance to the drug oxamniquine (OXA). The aim of the related article was to investigate the origin of OXA resistant mutations in the New Wolrd by identifying sequence variation in <em>SmSULT-OR</em> in <em>S. mansoni</em> from the Old World, where OXA has seen minimal usage.</p>
REVEL (Rare Exome Variant Ensemble Learner) Scores
<p>REVEL is an ensemble method for predicting the pathogenicity of missense variants in the human genome. For more information, see <a href="https://sites.google.com/site/revelgenomics/">https://sites.google.com/site/revelgenomics/</a> and <a href="https://dx.doi.org/10.1016/j.ajhg.2016.08.016">https://dx.doi.org/10.1016/j.ajhg.2016.08.016</a>.</p>
Exome sequence analysis identifies rare coding variants associated with a machine learning-based marker for coronary artery disease.
<p>*.sh and *.R are codes to test rare coding variants for association with ISCAD.</p> <p>Petrazzini_etal_2024_*_level_meta_analysis.txt.gz are summary statistics of variant- and gene-level associations of rare coding variants in the exome sequences of 604,914 individuals with an in-silico score for coronary artery disease (ISCAD).</p> <p>Chromosomal positions are mapped to the GRCh38 (hg38) human genome reference.</p> <p>Directions of effect correspond to associations in the UK Biobank, the All of Us Research Program, the BioMe Biobank sample 1 and the BioMe Biobank sample 2, in that order.</p>
Exome Sequencing Study in Cardiomyopathy to Identify New Risk Variants
ClinicalTrials.gov study NCT03754101. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum
Open the record for dataset details and reuse information.
Data from: Identification of novel variants in LTBP2 and PXDN using whole-exome sequencing in developmental and congenital glaucoma
Open the record for dataset details and reuse information.
Exome sequencing data analysis to characterize rare germline copy number variants involved in colorectal cancer predisposition
GEO Series GSE96597. Homo sapiens. 10 samples. Type: Expression profiling by array.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K5B)
GEO Series GSE252642. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Exome-wide rare loss-of-function variant enrichment study in 21,347 Han Chinese individuals identifies four new susceptibility genes for psoriasis [healthy controls]
GEO Series GSE131670. Homo sapiens. 12398 samples. Type: Genome variation profiling by array; SNP genotyping by SNP array.
Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss
GEO Series GSE64088. Homo sapiens. 308 samples. Type: Genome variation profiling by genome tiling array.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K6B)
GEO Series GSE252416. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
Exome sequencing data analysis to characterize copy number variants involved in m.14487T>C mutation
GEO Series GSE131740. Homo sapiens. 5 samples. Type: Other.
Exome-wide rare loss-of-function variant enrichment study in 21,347 Han Chinese individuals identifies four new susceptibility genes for psoriasis [psoriasis patients]
GEO Series GSE131663. Homo sapiens. 8949 samples. Type: Genome variation profiling by array; SNP genotyping by SNP array.
A novel approach for simultaneous detection of structural and single-nucleotide variants based on a combination of chromosome conformation capture and exome sequencing
GEO Series GSE253950. Homo sapiens. 70 samples. Type: Other; Expression profiling by high throughput sequencing.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K4B)
GEO Series GSE252687. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (K7B)
GEO Series GSE252344. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing; Other; Genome variation profiling by high throughput sequencing.
Whole Exome Sequencing in Finding Causative Variants in Germline DNA Samples From Patients With Hypertension Receiving Bevacizumab for Breast Cancer
ClinicalTrials.gov study NCT02610413. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Whole Exome Sequencing in Finding Causative Variants in Germline DNA Samples From Patients With Peripheral Neuropathy Receiving Paclitaxel for Breast Cancer
ClinicalTrials.gov study NCT02610439. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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International Brain Laboratory public data
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OpenNeuro
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