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Dataset results
37 results for “phenotypic features”
GWAS Summary Statistics for Publication: Identifying novel genetic and phenotypic associations to genomic features by leveraging off-target reads in exome sequencing data
<p>This dataset contains summary statistics for genome-wide association studies (GWAS) conducted on genomic features derived from off-target reads in whole-exome sequencing (WES) data. The study utilized tools like Seeing Beyond the Target (SBT) and ImReP to construct novel phenotypic features from unmapped reads in ~50,000 participants in the UK Biobank. Features include mitochondrial DNA (mtDNA) copy number, ribosomal DNA (rDNA) copy number (5S, 18S, 28S), immune repertoire metrics (e.g., T-cell receptor alpha diversity), and microvial genome load (viral and fungal).</p> <p>Summary statistics can be used for replication studies, meta-analyses, or further exploration of these phenotypes.</p>
Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
<p><span>How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species <em>Lumnitzera littorea</em> and <em>Lumnitzera racemosa</em> provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species <em>Combretum micranthum</em>. While most mangroves have small genomes, the genomes of both <em>Lumnitzera </em>species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, <em>Lumnitzera</em> species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, <em>Lumnitzera </em>genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the <em>Lumnitzera </em>species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.</span></p>
Exploring phenotypic diversity of pigmented traits and iris features in Pakistani population
<p><span>Phenotypic variations of eye color, skin color, and iris surface features have been well-explored in certain populations. However, there has been comparatively little research on variations in these features in Pakistani population. The aim of this study is to</span> discover phenotypic diversity and correlations of pigmented traits and iris surface features in Punjab and Khyber-Pakhtunkhwa (KPK)<b> </b>province of Pakistan<b>.</b> Digital images of eyes and skin were examined by investigators to determine color using Fitzpatrick Phototype Scale. Similarly, iris patterns were characterized by Edward iris feature software and association studies were conducted through SPSS program. Intermediate eye color was frequent in KPK (44%) while brown was higher in Punjab (47%). <span>Contrarily</span>, light to medium brown skin color was recurring (55%) in Punjab whereas lighter skin color prevailed in KPK (69%). Furthermore, Fuchs' crypts were significantly correlated with contraction furrows in both populations. Likewise, crypts were significantly associated with Wolfflin nodules and furrows were significantly related to conjunctival melanosis and pigment spots in KPK sample set. Based on unique iris patterns, these phenotypic traits would be helpful for individuals' discrimination in the population<b>. </b>In future, there is need to explore genetic associations and functional differences of these traits.</p>
Dataset related toa article: "Dystonia as a prominent feature of TCF20-associated neurodevelopmental disorder: Expanding the phenotype"
<p>Sanger sequences (.abi files) validating variants found with whole exome sequencing</p>
Exploring phenotypic diversity of pigmented traits and iris features in Pakistani population
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Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
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Natural history, phenotypic spectrum, and discriminative features of multisystemic RFC1-disease
<p>Objective: To delineate the full phenotypic spectrum, discriminative features, piloting longitudinal progression data, and sample size calculations of RFC1-repeat expansions, recently identified as causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS).</p> <p>Methods: Multimodal RFC1 repeat screening (PCR, southern blot, whole-exome/genome (WES/WGS)-based approaches) combined with cross-sectional and longitudinal deep-phenotyping in (i) cross-European cohort A (70 families) with ≥2 features of CANVAS and/or ataxia-with-chronic-cough (ACC); and (ii) Turkish cohort B (105 families) with unselected late-onset ataxia.</p> <p>Results: Prevalence of RFC1-disease was 67% in cohort A, 14% in unselected cohort B, 68% in clinical CANVAS, and 100% in ACC. RFC1-disease was also identified in Western and Eastern Asians, and even by WES. Visual compensation, sensory symptoms, and cough were strong positive discriminative predictors (>90%) against RFC1-negative patients. The phenotype across 70 RFC1-positive patients was mostly multisystemic (69%), including dysautonomia (62%) and bradykinesia (28%) (=overlap with cerebellar-type multiple system atrophy [MSA-C]), postural instability (49%), slow vertical saccades (17%), and chorea and/or dystonia (11%). Ataxia progression was ~1.3 SARA points/year (32 cross-sectional, 17 longitudinal assessments, follow-up ≤9 years [mean 3.1]), but also included early falls, variable non-linear phases of MSA-C-like progression (SARA 2.5-5.5/year), and premature death. Treatment trials require 330 (1-year-trial) and 132 (2-year-trial) patients in total to detect 50% reduced progression.</p> <p>Conclusions: RFC1-disease is frequent and occurs across continents, with CANVAS and ACC as highly diagnostic phenotypes, yet as variable, overlapping clusters along a continuous multisystemic disease spectrum, including MSA-C-overlap. Our natural history data help to inform future RFC1-treatment trials.</p>
Characterization of Bronchodilator Response in Children With Bronchiolitis Using Phenotypic and Genotypic Features
ClinicalTrials.gov study NCT06946264. IPD Sharing: YES. Countries: 1. Publications: 13.
Natural history, phenotypic spectrum, and discriminative features of multisystemic RFC1-disease
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SARS-CoV-2-specific T cells exhibit phenotypic features reflecting helper function, lack of terminal differentiation, and high proliferation potential
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Moderate intrinsic phenotypic alterations in C9orf72 ALS/FTD iPSC-microglia despite the presence of C9orf72 pathological features
GEO Series GSE233262. Homo sapiens. 68 samples. Type: Expression profiling by high throughput sequencing.
Seven chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
GEO Series GSE256256. Homo sapiens. 112 samples. Type: Other.
BRAFV600E induces key features of LCH in iPSCs with cell type–specific phenotypes and drug responses
GEO Series GSE270891. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
A pathogenic CD4 T cell phenotype in experimental uveitis shares common features with other immune mediated inflammatory diseases [EAU]
GEO Series GSE289821. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Distinguishing smoking related lung disease phenotypes via imaging and molecular features
GEO Series GSE132829. Homo sapiens. 146 samples. Type: Expression profiling by high throughput sequencing.
Opposing Effects of HIF1α and HIF2α on Chromaffin Cell Phenotypic Features and Tumor Cell Proliferation: Insights from MAX [human]
GEO Series GSE51081. Homo sapiens. 9 samples. Type: Expression profiling by array.
Opposing Effects of HIF1α and HIF2α on Chromaffin Cell Phenotypic Features and Tumor Cell Proliferation: Insights from MAX
GEO Series GSE51087. Rattus norvegicus; Homo sapiens. 13 samples. Type: Expression profiling by array.
Microencapsulated 3D co-cultures recapitulate phenotypic features of B lymphomas
GEO Series GSE178935. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging [RNA-Seq]
GEO Series GSE119318. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging [miRNA-Seq]
GEO Series GSE119319. Mus musculus. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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.