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Dataset results
69 results for “clonal analysis”
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Exome-wide association analysis (ExWAS) of clonal haematopoiesis in 136,401 Admixed Americans and 416,118 Europeans
<p>We performed exome-wide association analysis (ExWAS) of germline genetic variants identified from whole-exome sequencing (WES) to identify novel inherited genetic determinants of clonal haematopoiesis (CH). Here, we provide the summary statistics from ExWAS CH performed on Admixed Americans recruited to the Mexico City Prospective Study (MCPS), Europeans recruited to the United Kingdom Biobank (UKB), and cross-ancestry meta-analysis of Admixed Americans and Europeans. Analyses was performed with REGENIE software (Firth's logistic regression), Fisher's exact test, and METAL software (inverse variance-weighted average method to derive effect size and <em>P</em>-value method to derive P value), respectively.</p> <p> </p> <p>In version 1 of this repository, UKB variants (*_UKB.tsv) with minor allele frequency (MAF) 1% or more were uploaded. In version 2, this is now rectified so that rare variants with MAF of 0.1% or more were uploaded. This threshold now matches the MCPS (*_MCPS.tsv) and UKB-MCPS meta-analysis summary statistics (*_MCPS-UKB_meta-analysis.tsv)</p>
Gene-collapsing analysis of clonal haematopoiesis in 136,401 Admixed Americans and 416,118 Europeans
<p>We performed gene-collapsing (gene burden) analysis of germline genetic variants identified from whole-exome sequencing (WES) to identify novel inherited genetic determinants of clonal haematopoiesis (CH). Here, we provide the summary statistics from CH gene-collapsing analysis performed on Admixed Americans recruited to the Mexico City Prospective Study (MCPS), Europeans recruited to the United Kingdom Biobank (UKB), and cross-ancestry meta-analysis of Admixed Americans and Europeans. Analyses was performed with <span>Fisher'</span>s exact test (for MCPS and UKB analysis) and Cochran–Mantel–Haenszel test (for meta-analysis).</p>
Data from: Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant
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A meta-analysis of effects of physiological integration in clonal plants under homogeneous vs. heterogeneous environments
<p class="CxSpFirst"><span><b>Summary</b></span></p> <p class="CxSpMiddle"><span>1. Clonal plants play key roles in maintaining community productivity and stability in many ecosystems. Connected individuals (ramets) of clonal plants can translocate and share e.g. photosynthates, water and nutrients, and such physiological integration may affect performance of clonal plants both<a name="_Hlk51046980"> in heterogeneous and homogeneous environments. </a>However, we still lack a general understanding of whether or how physiological integration in clonal plants differs across homogeneous vs. heterogeneous environments. </span></p> <p class="CxSpMiddle"><span>2. We compiled data from 198 peer reviewed scientific studies conducted in 19 countries with 108 clonal plant species from 35 families, and carried out a meta-analysis of effects of physiological integration on 16 traits related to plant growth, morphology, physiology or allocation. Our analyses evaluated these relationships in A) heterogeneous environments where at least one resource essential for plant growth (e.g. light, soil water and mineral nutrients) or non-resource factor (e.g. grazing, trampling and burial) is spatially non-uniformly distributed, and B) homogeneous environments where all these factors are spatially uniformly distributed.</span></p> <p class="CxSpMiddle"><span>3. Physiological integration increased growth of whole clones in both homogeneous and heterogeneous environments due to its highly significant contribution to growth of recipient ramets. Integration did not affect growth of donor ramets in heterogeneous environments, but decreased it in homogeneous environments. </span></p> <p class="CxSpMiddle"><span>4. Integration affected physiological traits of donor ramets in neither homogeneous nor heterogeneous environments. It did not affect any physiological traits of recipient ramets in homogeneous environments, but increased most of them in heterogeneous environments. For donor ramets, integration increased height by 53% and internode length by 37% in heterogeneous environments, but had no effect in homogeneous environments. For recipient ramets, integration increased height by 73% in homogeneous environments and by 115% in heterogeneous environments, and increased internode length by 35% only under heterogeneous environments. In heterogeneous environments, integration increased biomass allocation to roots of donor ramets under high water/nutrient conditions and decreased it under high light. </span></p> <p>5. Physiological integration plays a strong role in clonal plant physiology, morphology, and growth, especially for recipient ramets in heterogeneous environments. Therefore, physiological integration may have contributed to the widespread of clonal plants in nature and their dominance in many ecosystems. It may also play important roles in invasion success of alien clonal plants and in maintaining functions and stability of ecosystems where clonal plants are abundant.</p>
Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.
A meta-analysis of effects of physiological integration in clonal plants under homogeneous vs. heterogeneous environments
Open the record for dataset details and reuse information.
Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system
Open the record for dataset details and reuse information.
Single-cell analysis reveals clonal expansions of pro-inflammatory tissue-resident memory Th17 cells in Crohn's disease
GEO Series GSE247264. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
Phenotypic and genomic analysis of multiple myeloma minimal residual disease clonal plasma cells: a new model to understand chemoresistance
GEO Series GSE70399. Homo sapiens. 30 samples. Type: Genome variation profiling by SNP array; Expression profiling by array.
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq II]
GEO Series GSE120358. Procambarus virginalis. 3 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish
GEO Series GSE112411. Procambarus virginalis; Procambarus fallax. 26 samples. Type: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Phenotypic, transcriptomic and genomic characterization of clonal plasma cells in light chain amyloidosis [Copy number analysis]
GEO Series GSE73041. Homo sapiens. 18 samples. Type: Genome variation profiling by SNP array.
Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [Exp 3]
GEO Series GSE194188. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Clonality analysis in breast tumour pairs using aCGH data
GEO Series GSE108984. Homo sapiens. 74 samples. Type: Genome variation profiling by genome tiling array.
An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Treg cells
GEO Series GSE292440. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Gene expression analysis of tumors of TN and R clonal pairs in vivo
GEO Series GSE139236. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
Clonal analysis of lineage fate in unperturbed hematopoiesis
GEO Series GSE90742. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Paired TCR and transcriptome analysis of single T cells characterizes clonally expanded human conventional and unconventional CD8+ T cells
GEO Series GSE107646. Homo sapiens. 921 samples. Type: Expression profiling by high throughput sequencing.
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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.