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402 results for “mtDNA”
Mitochondrial DNA (mtDNA) Data
<p>Dataset taken from https://sites.google.com/site/consensusmotifs/</p> <p>Stored on Zenodo as backup for Stumpy Consensus Motif Search</p>
Mitochondrial DNA (mtDNA) Data
<p>Dataset taken from https://sites.google.com/site/consensusmotifs/</p> <p>Stored on Zenodo as backup for Stumpy Consensus Motif Search</p>
The Greeks in the West - mtDNA dataset
<p>This dataset contains mitochondrial DNA data of the HVR-I region (range=16040-16569) of two Greek populations (Euboea island and Corinthia) and three Italian populations (East Sicily, Matera and Cosenza)</p>
Figure 2 in Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies
Figure 2. Illustration of steps in constructing a Random Forests ensemble of classification trees.
Raw data for Hancock-Cerutti et. al. "ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling"
<p>Blot images and tabular data for Hancock-Cerutti et. al. "ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling"</p>
Text-fig. 2. Scheme of position of primers on mtDNA D-loop (adopted from Gundry et al. 2007). in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 2. Scheme of position of primers on mtDNA D-loop (adopted from Gundry et al. 2007).
Figure 4 in Determination of genetic variations between Apodemus mystacinus populations distributed in Turkey inferred from mtDNA PCR-RFLP
Figure 4. UPGMA dendrogram of the composite data by combining cytb and D-loop regions.
From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel
<p>In this dataset we provide the 1000 Genomes Project's samples processed in our manuscript:</p> <p>Cortes-Figueiredo, F.; Carvalho, F.S.; Fonseca, A.C.; Paul, F.; Ferro, J.M.; Schönherr, S.; Weissensteiner, H.; Morais, V.A. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. <em>Int. J. Mol. Sci</em>. <strong>2021</strong>, <em>22</em>, 12031. <a href="https://doi.org/10.3390/ijms222112031">https://doi.org/10.3390/ijms222112031</a><em>.</em></p> <p><strong>Abstract</strong></p> <p>Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines.</p> <p><br> Please refer to our the github page <a href="https://github.com/filcfig/PCP.git">filcfig/PCP</a>, for more details on running the PrecisionCalllerPipeline.</p>
MinION sequencing data of mtDNA from BH10 cells
<p><span>Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic because of its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we have taken advantage of a cell model with two different types of mitochondrial genomes and impaired ability to turn over broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot. Combining our observations with previously published work, we propose that the mitochondrial replisome can catalyze microhomology-mediated recombination of linear mtDNA ends, thus rendering a specialized mitochondrial recombinase unnecessary. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.</span></p>
Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
<p><span>Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of </span><span>the latter</span><span> </span><span>two</span><span> revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary </span><span>histories,</span><span> we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-</span><span>western</span><span> Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 </span><span>radiocarbon-dated</span><span> samples for calibration of the molecular clock. We found that across the three </span><span>species,</span><span> divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response </span><span>of species adapted to open habitat to the interglacial environments. </span><span>In European narrow-headed voles, we identified multiple </span><span>time-structured</span><span> mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three </span><span>species,</span><span> allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.</span></p>
Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
<p><span>Assigning prehistoric objects to specific individuals is usually impossible outside of burial contexts. Here we present a non-destructive method for gradually releasing DNA from ancient bone and tooth artifacts. Application of the method to an Upper Paleolithic deer tooth pendant from Denisova Cave (Russia) resulted in the recovery of DNA from both the deer and a female human individual. Genetic dates obtained from the deer and human mitochondrial genomes estimate the age of the pendant at approximately 20,000 to 24,000 years. Nuclear DNA from its presumed maker or wearer shows strong affinities to contemporaneous Ancient North Eurasian individuals previously found further east in Siberia. Our work opens up new possibilities for linking cultural and genetic records in prehistoric archaeology.</span></p>
Aquaculture-driven evolution of the salmon louse mtDNA genome
<p><span>Resistance towards the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (<em>Lepeophtheirus</em> <em>salmonis</em> <em>salmonis</em>), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000–2002 "pre-resistance") and contemporary (2014–2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000–2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and, that long-distance dispersion of resistance is rapid due to the high level of genetic connectivity that is observed in this species.</span></p>
Collection_nsyn_human_mtDNA_in_cancer
<p>A collection of cancer-associated or somatic non-synonymous variants for human mitochondrial genome. Variants are ordered by genomic position. Clinical and molecular data are taken from public variant databases and recent literature about the possible involvement of mitochondrial protein coding genes on cancer development. Sheet 1: somatic variant dataset; sheet 2: description for each field. It could be useful for mitochondrial geneticists.</p>
Data for paper: Genomic data reveals new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)
<p>Files in this repository:</p><p>"COI_alignment.fas.zip" Zipped file of the FASTA alignment of the COI sequences.</p><p>"COI_IQtree.treefile" Newick treefile resulting from the IQ-tree analysis of the COI alignment.</p><p>"RAD-loci_alignment.nex.zip" Zipped file of the NEXUS alignment of RAD loci of 2295 samples.</p><p>"RAD-loci_IQtree.tre" Newick treefile resulting from the IQ-tree analysis of the RAD-loci alignment.</p><p>"RAD-SNP_alignment.usnps.nex" NEXUS alignment of the RAD-SNP data of 50 samples.</p><p>"RAD-SNP_SNAPP.trees" Set of Newick trees resulting from the BEAST SNAPP analysis.</p>
Aquaculture-driven evolution of the salmon louse mtDNA genome
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Multiple sequence alignments of newly reconstructed and published cervid and human mtDNA
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Data from: Population structure of mtDNA variation due to Pleistocene fluctuations in the South American maned wolf (Chrysocyon brachyurus, Illiger, 1815): management units for conservation
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Arthropod mtDNA paraphyly: a case study of introgressive origin
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MinION sequencing data of mtDNA from BH10 cells
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Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
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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.