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1,023 results for “copy number”
Data from: Dynamics of copy number variation in host races of the pea aphid
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Grs and Ors, respectively), in the process of host race formation. We used targeted re-sequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors, and a decrease in the probability of complete gene duplication or deletion (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Grs were over-represented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics (output data)
<p>This contains the output results of CalicoST (inferred CNAs and cancer clones), results of comparison methods, and CNAs inferred from WES data of 13 samples across four cancer types.</p> <p>In this updated version, we also included the simulated data and the results from CalicoST and other methods in CalicoST_simulation_deposit.zip. README contains the details of deposited files.</p>
Computational validation of clonal and subclonal copy number alterations from bulk tumour sequencing
<p>Somatic variant identification from WGS data is a crucial step in the analysis of cancer genomes. Several tools are available to perform mutations calling, however, the noisiness of data requires appropriate quality control assessment. In the preprint work available at https://doi.org/10.1101/2021.02.13.429885 we present CNAqc, an R package devised to assess the quality of allele-specific Copy Number Alterations (CNA), somatic mutations, and tumor purity estimates. In order to test the model, we ran CNAqc on 2778 single-sample PCAWG whole-genomes and 48 TCGA whole-exomes. We uploaded the results of our analysis using the release of the tool available at https://github.com/caravagnalab/CNAqc/releases/tag/rr_22_0.1 in the form of .rds files. All the necessary details for the reproduction of our results are reported in the Supplementary Materials of the above-mentioned manuscript.</p>
Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations
<p>A MySQL database for metabolomic signatures for The Northern Finland Birth Cohorts, <strong>NFBC1966 </strong>and <strong>NFBC1986</strong>, a longitudinal research program based at the Medical Faculty, University of Oulu, Finland. This dataset is a supplement to the manuscript titlted "Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations"</p>
Dataset for "Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer"
<p>Processed single cell whole genome sequencing data from:</p> <p>Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer Williams, Vinci Oliphant et al 2024</p> <p>Included are processed copy number profiles for all cells included in the study.</p>
Whole Proteome Copy Number Dataset in Primary Mouse Cortical Neurons
<p>Raw data-Supplementary table- "Whole Proteome Copy Number Dataset in Primary Mouse Cortical Neurons"</p>
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
<p>Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (<a href="https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts">https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts</a>).</p>
Postprandial Effect of High-starch Meals in Individuals With Low and High Copy Number of the Salivary Amylase Gene
ClinicalTrials.gov study NCT03974126. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
SMN Copy Number Distribution in Mali, West Africa
ClinicalTrials.gov study NCT01059240. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Prenatal Cytogenetic Diagnosis by Array-Based Copy Number Analysis
ClinicalTrials.gov study NCT01279733. IPD Sharing: Not stated. Countries: 1. Publications: 1.
NanoString nCounter copy number variation assay
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Data from: Copy number variation and expression analysis reveals a nonorthologous pinta gene family member involved in butterfly vision
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Data from: Peripheral blood mitochondrial DNA copy number is associated with prostate cancer risk and tumor burden
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Impact of the POLRMT inhibitor IMT1B on mitochondrial genome copy number in Caenorhabditis elegans
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Avian MHC copy number variation is associated with helminth richness
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Data from: Dynamics of copy number variation in host races of the pea aphid
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Data from: Distribution and functionality of copy number variation across European cattle populations
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
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Table S1.- Occurrence analysis in alpha-proteobacteria, represented by number of copies of each gene on strain genome.
<p>Data set of 204 alphaproteobacteria to analyze for the presence and absence of 12 proteins related to the pantothenate synthesis and transport. The protein FASTA files (faa) for each of the genomes were downloaded from the RefSeq NCBI database. Protein sequences with an expectation value (E) of 10<sup>-3</sup>or less were considered as putative homologues. We used Proteinortho v5.15 to obtain the clusters of orthologous proteins from the 204 protein FASTA files. Next, we used the Pfam v31.0 database to determine which protein ortho clusters represent the 12 proteins of interest analyzed in this work. The proteins we searched for were: PYD1, PYD2, PYD3, GAD, KPHMT, PS, ADC, KPR, MRF, KAR, Aam and GabT.</p>
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.