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.
44
datasets available to search
ShareScore release 0.9.0
Dataset results
44 results for “mutation spectrum”
Bedrock radioactivity influences the rate and spectrum of mutation - Orthologous genes
<p>Alignments of the 2490 orthologous genes used in the article "Natural Bedrock radioactivity influences the rate and spectrum of mutation" to estimate the mutational spectrum and synonymous substitution rate.</p> <p>To compute accurate synonymous substitution rate, we removed genes with short sequences (<half of the alignment) and genes strongly supporting another phylogeny using ProfileNJ <a href="https://paperpile.com/c/Klqlpb/W5sS">(Noutahi et al. 2016)</a> with a bootstrap threshold of 90%, resulting in a subset of 769 genes listed in the file "List_769_1-to-1_orthologs_EvolutionRate.txt".</p> <p>Transcriptome paired-end reads used to define these orthologous genes have been deposited to the European Nucleotide Archive and are available under the study ID PRJEB14193.</p> <p>Sequences were aligned with Prank<a href="https://paperpile.com/c/Klqlpb/pilh"> (Löytynoja & Goldman 2008)</a> using a codon model and sites ambiguously aligned were removed with Gblocks <a href="https://paperpile.com/c/Klqlpb/c5kb">(Castresana 2000)</a>.</p>
Data files associated with: Evolution of the mutation spectrum across a mammalian phylogeny
Open the record for dataset details and reuse information.
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in mycosis fungoides and Sezary syndrome
<p>T-cell non-Hodgkin's lymphomas (NHL) develop following transformation of tissue resident T-cells. We performed a meta-analysis of mutational catalogues derived from whole exome sequencing data from 403 patients with eight subtypes of T-cell NHL to identify mutational signatures and recurrent gene mutations associated with specific causal peaks within these signatures. Signature 1, indicative of age-related deamination, was prevalent across all T-cell NHL subtypes, reflecting the derivation of these malignancies from memory T-cell subsets. Adult T-cell leukemia-lymphoma (ATLL) was specifically associated with signature 17, which was found to strongly correlate with the IRF4 K59R mutation that is exclusive to ATLL. Signature 7, implicating UV exposure as a potential initiating factor was uniquely identified in cutaneous T-cell lymphoma, contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4+ T-cells isolated from blood suggesting extensive re-circulation of these T-cells through both skin and blood and strongly implicating a role for UV in the pathogenesis of cutaneous T-cell lymphoma.</p>
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
<p>Although studies of <em>Saccharomyces cerevisiae</em> have provided many insights into mutagenesis and DNA repair, most of this work has focused on a few laboratory strains. Much less is known about the phenotypic effects of natural variation within <em>S. cerevisiae</em>'s DNA repair pathways. Here, we use natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated <em>S. cerevisiae</em> strains. To determine whether these differences are likely caused by genetic mutation rate modifiers, we use a modified fluctuation assay with a <em>CAN1</em> reporter to measure de novo mutation rates and spectra in 16 of the analyzed strains. We measure a 10-fold range of mutation rates and identify two strains with distinctive mutation spectra. These strains, known as AEQ and AAR, come from the panel's 'Mosaic beer' clade and share an enrichment for C > A mutations that is also observed in rare variation segregating throughout the genomes of several Mosaic beer and Mixed origin strains. Both AEQ and AAR are haploid derivatives of the diploid natural isolate CBS 1782, whose rare polymorphisms are enriched for C > A as well, suggesting that the underlying mutator allele is likely active in nature. We use a plasmid complementation test to show that AAR and AEQ share a mutator allele in the DNA repair gene <em>OGG1</em>, which excises 8-oxoguanine lesions that can cause C > A mutations if left unrepaired.</p>
dataset related to article "EXPANDING THE GENETIC SPECTRUM OF PRIMARY FAMILIAL BRAIN CALCIFICATION DUE TO SLC2OA2 MUTATIONS: A CASE SERIES"
<p>Sanger sequences (.abi files) of all patients of our Fondazione Besta Cohort.</p>
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
<p>Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of <i>de novo</i> mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (<i>Microcebus</i> <i>murinus</i>), we estimated the mutation rate to be 1.52 × 10<sup>–8</sup> (95% credible interval: 1.28 × 10<sup>−8</sup> to 1.78 × 10<sup>−8</sup>) mutations/site/generation, a rate among the highest calculated for a mammal. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false negative and false positive rate for our data and show that any point estimate of a <i>de novo </i>mutation rate should be considered with a large degree of uncertainty. To validate these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which <i>de novo</i> mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution rate analyses for all species compared.</p>
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in mycosis fungoides and Sezary syndrome
Open the record for dataset details and reuse information.
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
Open the record for dataset details and reuse information.
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
Open the record for dataset details and reuse information.
Data from: The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight to the evolutionary mutation spectrum
A long-standing question in evolutionary biology asks whether the genetic changes contributing to phenotypic evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within a population of Mimulus lewisii. To determine whether these types of changes are predictable, we combined this information with data from other species to investigate whether the spectrum of mutations affecting flower color transitions differs based on the evolutionary time-scale since divergence. We used classic genetic techniques, along with gene expression and population genetic approaches, to identify the putative, loss-of-function mutation that generates rare, white flowers instead of the common, pink color in M. lewisii. We found that a frameshift mutation in an anthocyanin pathway gene is responsible for the white-flowered polymorphism found in this population of M. lewisii. Comparison of our results with data from other species reveals a broader spectrum of flower color mutations segregating within populations relative to those that fix between populations. These results suggest that the genetic basis of fixed differences in flower color may be predictable, but that for segregating variation is not.
Evaluation of Somatic Mutation Spectrum as Biomarker for Survival Outcome in Chinese CRC
ClinicalTrials.gov study NCT04228614. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Investigation of Tumour Spectrum of Germline Mutations in Breast and Ovarian Cancer Genes.
ClinicalTrials.gov study NCT03246841. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: Disentangling the influence of mutation and migration in clonal seagrasses using the Genetic Distance Spectrum for microsatellites
Open the record for dataset details and reuse information.
Data from: The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight to the evolutionary mutation spectrum
Open the record for dataset details and reuse information.
Data from: Limited role of generation time changes in driving the evolution of the mutation spectrum in humans
Open the record for dataset details and reuse information.
Data used in the article "Bedrock radioactivity influences the rate and spectrum of mutation"
<p>Data used in the article entitled ‘Bedrock radioactivity influences the rate and spectrum of mutation’ by Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny-Dupré, David Eme, Arnaud Bellec, Vincent Breton, Laurent Duret, Tristan Lefébure and Christophe J. Douady.</p> <p>Table 1: Description of sampling sites (species found and measurements of radioactivity).</p> <p>Table 2: Raw activity for each radionuclide in the selected sites</p> <p>Table 3: Computational methods to model the effective dose of radioactivity.</p> <p>Table 4: Corrected activity for each radionuclides.</p> <p>Table 5: Number of reads for each sequenced transcriptome</p> <p>Table 6: Mutation counts for each type of mutation, computed on all positions.</p> <p>Table 7: Mutation counts for each type of mutation, computed on third positions.</p> <p>Table 8: Relative frequency for each type of mutation, computed on all positions.</p> <p>Table 9: Relative frequency for each type of mutation, computed on third positions.</p> <p> </p> <p> </p> <p> </p>
Homologous Recombination Repair Pathway Gene Mutation Spectrum in Chinese Breast Cancer Patients
ClinicalTrials.gov study NCT05901025. IPD Sharing: NO. Countries: 0. Publications: 9.
Data from: Neurologic phenotypes associated with COL4A1/2 mutations: expanding the spectrum of disease
Open the record for dataset details and reuse information.
Biallelic PAX5 mutations cause hypogammaglobulinemia,sensorimotor deficits and autism spectrum disorder
GEO Series GSE182463. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons
GEO Series GSE122550. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
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.