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42 results for “Clonal lineage”
DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures.
<p>The following depository contains raw phenotypic data and intermediate DNA methylation data presented in the article <strong>"DNA methylation in clonal Duckweed lineages (<em>Lemna minor </em>L.) reflects current and historical environmental exposures.</strong>" :</p> <p><strong>1) Raw phenotypic data</strong></p> <p>- Frond_area_Phase1_Phase2 -> Frond area measured at different time points (week 1, 6, 7 and 8) during the experiment.</p> <p>- Frond_number_Phase1_Phase2 -> Frond number measured at different time points (week 1, 6, 7 and 8) during the experiment.</p> <p><strong>2) Intermediate files obtained from running the epiGBS2 pipeline. The following files are available:</strong></p> <p>- consensus_cluster.renamed.fa -> epiGBS <em>de novo </em>loci. This file consists of the <em>de novo </em>epiGBS reference sequence file obtained during the <em>de novo </em>reference creation.</p> <p>- methylation.filtMETH -> The filtered DNA methylation data. This data was obtained after filtering the raw DNA methylation data. Cytosines which had a 10X coverage or higher and which were present in 80% of all samples were kept for further analysis.</p> <p>Demultiplexed and raw data were deposited at NCBI: BioProject: <strong>PRJNA883550</strong></p>
Data for Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data
<p>This is the accompanying data to the manuscript titled<em> Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data</em>. To reproduce the TRIBAL output please use this <a href="https://doi.org/10.5281/zenodo.12741290">code repository</a> as the arguments and codebase may have changed since release. </p>
Data from: What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen
Range-expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty-seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analyzing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15°C and more slowly at 28 and 32°C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade-off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.
Data from: What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen
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Dataset and Scripts for: Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus
<p>Dataset and Scripts for the research article: Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus.</p> <p>A git repository can be found at: <a href="https://gitlab.com/smlatorreo/genetic_history_of_rice-infecting_magnaporthe_oryzae">https://gitlab.com/smlatorreo/genetic_history_of_rice-infecting_magnaporthe_oryzae</a></p>
Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R
Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs, and (iv) describing several spatial components of clonality. RClone allows the one shot analysis of multi-population datasets without size limitation, suitable for datasets now increasingly produced through Next Generation Sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClone_quickmanual) or several populations (RClone_qmsevpops).
Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations
Understanding how diversity emerges in a single niche is not fully understood. Rugged fitness landscapes and epistasis between beneficial mutations could explain coexistence amongst emerging lineages. To provide an experimental test of this notion, we investigated epistasis amongst four pleiotropic mutations in rpoS, mglD, malT and hfq present in two coexisting lineages that repeatedly fixed in experimental populations of Escherichia coli. The mutations were transferred into the ancestral background individually or in combination of double or triple alleles. The combined competitive fitness of two or three beneficial mutations from the same lineage was consistently lower than the sum of the competitive fitness of single mutants – a clear indication of negative epistasis within lineages. We also found sign epistasis (i.e. the combined fitness of two beneficial mutations lower than the ancestor), not only from two different lineages (i.e. hfq and rpoS) but also from the same lineage (i.e. mglD and malT). The sign epistasis between loci of different lineages indeed indicated a rugged fitness landscape, providing an epistatic explanation for the coexistence of distinct rpoS and hfq lineages in evolving populations. The negative and sign epistasis between beneficial mutations within the same lineage can further explain the order of mutation acquisition.
Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However: tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato-specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato-specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists.
Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R
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Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Open the record for dataset details and reuse information.
Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations
Open the record for dataset details and reuse information.
Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade [scRNA-seq]
GEO Series GSE185204. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing; Other.
Clonal barcoding of endogenous adult hematopoietic stem cells reveals a spectrum of lineage contributions
GEO Series GSE246271. Mus musculus. 80 samples. Type: Other.
Clonal lineage tracing and transcriptomics of cortical progenitor populations reveal maintenance of differentiation potential.
GEO Series GSE283411. Mus musculus. 5 samples. Type: Other; Expression profiling by high throughput sequencing.
Inflammatory neuropathy driven by a pathologically expanded, clonal lineage of IL-21 producing CD4+ T cells [scRNA-seq]
GEO Series GSE252646. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Clonal conversion of B-lymphoid leukemia reveals cross-lineage transfer of malignant states.
GEO Series GSE90655. Mus musculus. 85 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy 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.
Mapping of clonal lineages across developmental stages in human neural differentiation (Biological Replicates #2 and #3)
GEO Series GSE221592. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing; Other.
Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade [scTCR-seq]
GEO Series GSE185205. Homo sapiens. 36 samples. Type: Other.
Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees
GEO Series GSE272588. Mus musculus. 605 samples. Type: Other; 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)
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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.