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datasets available to search
ShareScore release 0.9.0
Dataset results
29 results for “Variant genotypes”
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
GEO Series GSE155983. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array
GEO Series GSE55134. Canis lupus familiaris. 351 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
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.
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>
Genotype -Phenotype Correlation of PKLR Variants With Pyruvate Kinase, 2,3-Diphosphglycerate and Adenosine Triphosphate Activities in Red Blood Cells of People With Sickle Cell Disease
ClinicalTrials.gov study NCT03685721. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis [RNA-Seq]
GEO Series GSE232336. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]
GEO Series GSE164938. Homo sapiens. 20 samples. Type: Genome variation profiling by SNP array.
Massively parallel analysis of genotype-dependent enhancer activity among atopic dermatitis genetic risk variants
GEO Series GSE300756. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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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.