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219
datasets available to search
ShareScore release 0.7.1
Dataset results
219 results for “genotyping‐by‐sequencing”
Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)
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Whole genome re-sequencing of mother and offspring D. magna genotypes
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Data from: Genotyping-in-Thousands by Sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon
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Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
GEO Series GSE125162. Saccharomyces cerevisiae. 12 samples. Type: Expression profiling by high throughput sequencing.
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
GEO Series GSE165845. Homo sapiens. 360 samples. Type: Genome variation profiling by array.
Integrative genotyping of cancer and immune phenotypes by long-read sequencing
GEO Series GSE243227. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
Multimodal sequencing (gene expression, chromatin accessibility, and mtDNA genotyping) of single cells of the RPE and choroid in human MELAS (m.3243A>G) and control samples
GEO Series GSE202886. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.
GEO Series GSE199625. Arabidopsis thaliana. 12 samples. Type: Methylation profiling by high throughput sequencing.
Analyzing whole genome bisulfite sequencing data from highly divergent genotypes
GEO Series GSE87101. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
Long-Read Single-Cell RNA Sequencing Enables Cell Genotyping to Refine Subclone Detection in Chronic Lymphocytic Leukemia
GEO Series GSE259253. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Genotyping]
GEO Series GSE130421. Homo sapiens. 3 samples. Type: Other.
Laser-capture microdissection and RNA sequencing of aleurone and starchy endosperm of maize R1 genotypes
GEO Series GSE200905. Zea mays. 18 samples. Type: Expression profiling by high throughput sequencing.
Genotyping of E14 mouse embryonic stem cells by sequencing
GEO Series GSE53149. Mus musculus. 2 samples. Type: Other; Methylation profiling by high throughput sequencing.
High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.
GEO Series GSE212945. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping)
GEO Series GSE56685. Homo sapiens. 30 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis - SNP Genotype Database
GEO Series GSE114518. Sus scrofa. 48 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
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: Cost effective microsatellite isolation and genotyping by high throughput sequencing
High throughput sequencing (HTS) has emerged as a valuable tool for the rapid isolation of genetic markers for population genetics and pedigree analysis. HTS-based SNP (single nucleotide polymorphism) genotyping protocols like RAD (Restriction-site associated DNA) sequencing or hybrid capture, allow for the isolation of thousands of markers from any non-model organism. However, these protocols are relatively laborious and expensive and the resulting high marker density is not always necessary. Since HTS technology has also greatly simplified the isolation and genotyping process of microsatellite markers, we develop microsatellite markers as a cost efficient and simple alternative to SNP genotyping. We present low coverage genome sequencing data from seven distantly related spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus, Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium, Theridion grallator) and show the utility of HTS for microsatellite isolation. We also present a simple Illumina amplicon sequencing protocol to genotype microsatellites from multiplex PCR amplicons in the Hawaiian happy face spider T. grallator. We discuss advantages and drawbacks of the use of microsatellites for a range of research questions, and highlight an unexpectedly fast decay and gain of repeat loci for T. grallator.
Optimization of HIV-1 DNA Genotyping by High Throughput Sequencing to Document Antiretroviral Resistant Mutations
ClinicalTrials.gov study NCT03512795. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Whole Genome Sequencing for Blood Group Genotyping and Definition as Exemplified on U- and St(a)+.
ClinicalTrials.gov study NCT02534519. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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)
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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.