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490 results for “DNA integrity”
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. (Continued).
Multi-omic integration of DNA methylation and gene expression data reveals molecular vulnerabilities in glioblastoma (processed data)
<p>Glioblastoma multiforme (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of GBM patients has led to an improved categorisation into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome-wide multi-omic approaches to identify potential molecular vulnerabilities existing in GBM patients. Integration of gene expression and DNA methylation data from both bulk GBM and patient-derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype-specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP1, SMAD3 and RUNX1 / RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype-specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal-like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.</p>
Impact of Sperm DNA Integrity on In Vitro Cycles
ClinicalTrials.gov study NCT01232465. IPD Sharing: Not stated. Countries: 1. Publications: 12.
Expanded phylogeny of Nomadinae (Hymenoptera: Apidae) with integration of UCE and DNA barcode sequence data
Open the record for dataset details and reuse information.
Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling
Open the record for dataset details and reuse information.
Data from: Integrating environmental DNA metabarcoding and remote sensing reveals known and novel fish diversity hotspots in a World Heritage Area
Open the record for dataset details and reuse information.
Datasets from PhD thesis: "Integrating classical and DNA-based approaches to advance the field of paleolimnology: Case studies of a warm monomictic lake"
<p>The general objectives of my PhD were to evaluate the advantages and limitations to using DNA-based methods in paleolimnology and to evaluate the ecological trajectory of Cultus Lake, British Columbia, using both classical paleolimnological and DNA-based approaches. The datasets therein were generated for my PhD thesis.</p> <p>Firstly, a 36-month sediment trap time series was developed to evaluate which DNA taxa can be deposited in the sediments and potentially be used as indicator taxa in paleolimnological studies. Congruence between morphological and DNA identification in water and sediment trap samples was also assessed specifically for diatoms and crustaceans. The data generated include mass accumulation rate and carbon accumulation rate, carbon and nitrogen percentage, morphological counts for diatoms and cladocerans in the sediment traps, DNA quantity for water and sediment trap samples, metabarcoding of a fragment of the V7 region of the 18S rRNA gene.</p> <p>Secondly, a multi-proxy paleolimnological study was developed to evaluate the ecological changes in Cultus Lake and the potential drivers of the changes. From this study, sedimentary delta 15N, delta 13C, percentage of carbon, percentage of nitrogen, pigments were measured and diatoms and cladoceran remains were counted and identified from a sediment core collected in 2008. The data for this project are part of a publication accepted in May 2020 in Journal of Paleolimnology: Gauthier et al (In press) Ecological dynamics of a peri-urban lake: a multi-proxy paleolimnological study of Cultus Lake (British Columbia) over the past ~200 years. doi: 10.1007/s10933-020-00147-9.</p> <p>Thirdly, a paleo-genetic project was developed to compare the ecological changes observed with sedimentary DNA with those observed with classical paleolimnological approaches. The same fragment of the V7 region of the 18S rRNA gene was targeted, percentage of carbon and nitrogen were also measured as well as DNA quantity for all intervals subsampled in a sediment core collected in 2017.</p> <p>The datasets usually come with a description of the data and meaning of abbreviations whether needed. DNA datasets will be publicly released upon acceptance of the manuscripts. For more information about the projects, methods and results, please refer to my PhD thesis published at McGill University. The number in front of the name of each file represents the chapter for which the data were generated.</p>
Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds
<p><b>The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds amongst the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.</b></p>
Data from: Integrative taxonomy at work: DNA barcoding of taeniids harbored by wild and domestic cats
In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless due to the poor quality of samples. These situations are frequent in parasitology. Here we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free-ranging domestic cats (F. s. catus) and their hybrids populations. Adult taeniids were collected by post-mortem examinations of the hosts, and morphologically identified as Taenia taeniaeformis. We produced the cox1 barcode sequences for all the analyzed specimens and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology-based approaches and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already described taeniid species. Indeed, we detected three well-defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.
FIGURE 28 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURE 28. Phylogram of the tree obtained using GARLI and with cox1 data for Neobidessodes alone. Node support, when above 50%: bold (GARLI bootstrap), normal font (TNT parsimony jackknife values). Abbreviations behind N. thoracicus sp.n.: "b.s" = black specimens; "l.f." = "light form".
FIGURES 36–41 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURES 36–41. Habitats of Neobidessodes: 36) NT, Kakadu NP, Creek on the way to Gunlom (NT 16), habitat of black specimens and the typical form of Neobidessodes thoracicus sp.n.; 37) Restpools in river at Gungurrul Lookout in Kakadu NP, October 1996, habitat of N. denticulatus, N. flavosignatus, N. mjobergi and N. thoracicus sp.n.; 38) S QLD, 8 km SE Miriam Vale, road to Agnes Water, Oyster Creek (QLD 50), habitat of N. denticulatus; 39) S QLD, N Brisbane, Caboolture/Beerburrum road, near King John Creek (QLD 62), shallow roadside swamp, habitat of N. denticulatus; 40) S NSW, 6.5 km SW Eden, Towamba Road 2 km N Nullica, 556 m (NSW 111), habitat of N. bilita; 41) S VIC, Simpsons Creek 12 km SW Orbost at Princess Hwy (VIC 116), habitat of N. bilita (Photos: L. Hendrich).
FIGURE 29 in The epigean Australasian species of Neobidessodes gen.n. diving beetles- a revision integrating morphology, cybertaxonomy, DNA taxonomy and phylogeny (Coleoptera: Dytiscidae, Bidessini)
FIGURE 29. Performance of clustering in Neobidessodes. The blue graph indicates the number of clusters relative to the number of a priori identified morphospecies, found at 1–10% preset clustering distance in SpeciesIdentifier software. The red graph depicts the percentage of clusters that contain one and only one a priori identified morphospecies relative to the number of a priori identified morphospecies. Perfect clustering performance would see both graphs at 100% at least in one interval (e.g. 3%).
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.