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.
10
datasets available to search
ShareScore release 0.9.0
Dataset results
10 results for “SNV”
SNV protocols example datasets for mOTUs v3
<p>Example datasets for the SNV protocols</p>
Filtered and annotated SNV and indel variants in the PC3 and LNCaP human prostate cancer cell lines
<p>150bp paired-end reads (insert size 350bp) were obtained using the Illumina HiSeqX sequencer. Samtools v1.3.1 mpileup and bcftools were used to interrogate indexed BAM files, from whole-genome reads aligned to human reference genome GRCh38 build 82, and generate a VCF (Variant Call Format) file of single nucleotide variants (SNVs) and short indel variants. Variants private, or unique to a particular cell line, or shared by both were next identified. Variants (likely to be common germline variants) present in HapMap, 1000 genomes phase 3 (2,504 human genomes), and the National Heart Lung and Blood Institute’s Exome Sequencing Project (ESP) (bundled variant data file available at https://goo.gl/mEogvD) were excluded. Variant files (VCF) were filtered using SnpSift with the following parameters: 'QUAL \textgreater= 200 \&\& DP \textgreater= 30', where QUAL denotes minimum variance confidence and DP total depth threshold. Filtered variants were annotated using SnpEff v4.3g. Please see https://github.com/sciseim/PCaWGS for associated scripts.</p> <p> </p>
Synthetic benchmarking data from "Comprehensive Benchmarking of SNV Callers for Highly Admixed Tumor Data"
<p>Synthetic benchmarking data simulating heterogeneous and admixed tumor data with implanted SNVs and indels at different admixture levels (0% to 90%) for targeted sequencing (exome and targeted gene panel).</p>
Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands
<p>Common SNPs from gnomAD</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
<p class="MsoNormal"><span>We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from an F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies</span><span>. To </span><span>demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of three true albino bison and 45 wild-type pelage color bison. Through the examination of genomic </span>variants fixed in the albino cohort and absent in the controls<span>, we identified a nonsynonymous</span> single nucleotide polymorphism (SNP) <span>mutation on chromosome 29 </span>in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provide a highly robust and informative resource for <span>genomics </span>investigations for this iconic North American species.</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
Open the record for dataset details and reuse information.
Effect of PTCHD1 SNV and truncating variants on gene expression during differentiation of iPSCs to neural progenitor cells
GEO Series GSE227711. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [SNV]
GEO Series GSE317918. Homo sapiens. 24 samples. Type: Genome variation profiling by array.
Diagnosis of Alzheimer's disease specific phospholipase c gamma-1 SNV by deep-learning based approach for high throughput screening
GEO Series GSE151270. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
SNV microarray data from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al
GEO Series GSE121844. Homo sapiens. 11 samples. Type: Genome variation profiling by SNP array.
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.