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19,342 results for “Sequence”
Direct nanopore sequencing of human cytomegalovirus ge-nomes from high-titre clinical samples
<p>This archive contains the nanopore generated HCMV genomes from the urine and lung clinical samples. The illumina derived genome sequences have been uploaded to GenBank as they are of higher quality, the nanopore sequences are uploaded here to avoid duplication on GenBank. Raw FASTQ reads from the virus are uploaded to NCBI SRA. The full paper abstract is given below. Nanopore sequencing is becoming increasingly commonplace in clinical settings, particularly for diagnostics and outbreak investigations. Its portability, low cost and ability to operate in near real-time has propelled it to the forefront of the recent SARS-CoV-2 pandemic. Although high sequencing error rates initially hampered its wider implementation, improvements have continually been made with each iteration of the nanopore flow cells and base calling software. Here, we assess the feasibility of using nanopore sequencing to determine the complete genome of human cytomegalovirus (HCMV) present in high-titre clinical samples without viral DNA enrichment, PCR amplification or prior knowledge of the sequences. We utilised a hybrid bioinformatic approach that involved assembling the reads<em> de novo</em>, improving the <em>de novo</em> consensus through alignment of reads to the best-matching genome from a collated set of published genomes, and polishing the improved consensus. The final consensus genome sequences from a urine and a lung sample, the latter with an HCMV to human DNA load approximately 50 times lower than the former, achieved 99.97 and 99.93% identity, respectively, to the bench-mark consensuses obtained independently by Illumina sequencing. Thus, we demonstrate that nanopore sequencing is capable of determining HCMV genomes directly from high-titre clinical samples with high accuracy. </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>
Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease
<p>Raw peptide microarray data of fluorescence intensities representing relative binding of antibodies in sera samples collected from different cohorts of patients diagnosed with a number of viral infections. Healthy controls are also included.</p> <p>Columns:</p> <p>Sequence - peptide sequence</p> <p>HCV - Hepatitis Virus C</p> <p>Dengue - Dengue virus</p> <p>WNV - West Nile Virus</p> <p>HBV - Hepatitis Virus B</p> <p>Chagas - Chagas disease</p> <p>ND - negative/healthy donor</p> <p>LowCV - low coefficient of variation</p> <p>HighCV - high coefficient of variation</p>
The biodegaration of dimethoate by S. marcescens and DNA sequences
<p>The biodegaration of dimethoate by S. marcescens; DNA sequence; MBL gene expression; survival ship of bacteria to insects</p>
Minion sequencing experiment, Macoma balthica, Vancouver BC
<p>Results from Minion sequencing experiment, for Macoma balthica from Vancouver BC. </p> <p>Pool of 10 individuals. Target : mitochondrial genomes. </p> <p>Vancouver_2023-03-16.tar.gz contains the raw data. </p> <p>fastq_runid_5b77d028c5e2872dda6946458aed8ae808cd60f8_[0to3]_0.fastq.gz are the base-called data (guppy, fast). </p>
DATA for Exploration of O-GlcNAc-transferase (OGT) glycosylation sites reveals a target sequence compositional bias
<p>Mass spectrometry data for identification of glycosylation sites in CBP ID3 and EWS LCRn</p> <p>Perl based implementation of glycosylation Site Predictor OGTcomPred</p>
Effect of different types of sequence data on palaeognath phylogeny
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and ele- phant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic re- lationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements, introns, and ultraconserved elements. Using the noncoding loci to- gether with protein-coding loci, this study investigated the factors that affected gene tree estimation error and the relation- ships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene tree–based approaches supported rheas as the group that diverged first among groups (1)–(4). Whereas gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees oc- curred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than noncoding loci. Regarding the relationships of (1)–(4), the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogeneous model and sug- gested the clustering of kiwi and cassowaries and emu the most likely with ∼40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.</p> </div> </div> </div>
The number of glyphosate resistant seeds produced by each of three bee species as they visit alfalfa flowers in sequence during a foraging bout
<p>Since the release of genetically engineered (GE) crops, there has been increased concern about the introduction of GE genes into non-GE fields of a crop and their spread to feral or wild cross-compatible relatives. More recently, attention has been given to the differential impact of distinct pollinators on gene flow, with the goal of developing isolation distances associated with specific managed pollinators. To examine the differential impact of bee species on gene movement, we <span>quantified the relationship between the probability of getting a GE seed in a pod, and the order in which a flower was visited, or the cumulative distance traveled by a bee in a foraging bout. We refer to these relationships as 'seed curves' and compare these seeds curves among three bee species. </span>The experiments used <em><span>Medicago sativa</span></em><span> L. plants carrying three copies of the glyphosate resistance (GR) allele as pollen donors (<em>M. sativa</em> is a tetraploid), such that each pollen grain carried the GR allele, and conventional plants as pollen recipients. </span><span>Different foraging metrics, including the number of GR seeds produced over a foraging bout, were also quantified and contrasted among bee species. The lowest number of GR seeds set per foraging bout, and the GR seeds set at the shortest distances, were produced following leafcutting bee visits. In contrast, GR seeds were found at the longest distances following bumble bee visits. Values for honey bees were intermediate. The ranking of bee species based on seed curves correlated well with field-based gene flow estimates. Thus, differential seed curves of bee species, which describe patterns of seed production within foraging bouts, translated into distinct abilities of bee species to move genes at a landscape level. Bee behavior at a local scale (foraging bout) helps predict gene flow and </span><span>the spread of GE genes at the landscape scale. </span></p>
Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)
<p>Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.</p>
Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue
<p><span>Influenza A viruses in animal reservoirs repeatedly cross species barriers to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human-to-human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans, and canine respiratory tract expresses both SAα2,3-(avian type) and α2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses were transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canines offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in worldwide</span> <span>over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SAα2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canines may serve as an intermediate for the adaptation of avian influenza virus to humans. Continuous surveillance coordinated with risk assessment for CIVs is necessary.</span></p>
Traing Data for "Assembly of metagenomic sequencing data" tutorial
<p>Metagenomics involves the extraction, sequencing and analysis of combined genomic DNA from <strong>entire microbiome</strong> samples. It includes then DNA from <strong>many different organisms</strong>, with different taxonomic background.</p> <p>Reconstructing the genomes of microorganisms in the sampled communities is critical step in analyzing metagenomic data. To do that, we can use <strong>assembly</strong> and assemblers, <em>i.e.</em> computational programs that stich together the small fragments of sequenced DNA produced by sequencing instruments.</p> <p>Assembling seems intuitively similar to putting together a jigsaw puzzle. Essentially, it looks for reads “that work together” or more precisely, reads that overlap. Tasks like this are <strong>not straightforward</strong>, but rather complex because of the complexity of the genomics (specially the repeats), the missing pieces and the errors introduced during sequencing.</p> <p>In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: <a href="https://www.ebi.ac.uk/metagenomics/studies/MGYS00005630#overview">Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem</a>. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.</p> <p>Based on the 6 original dataset of the coffee fermentation system, we generated mock datasets for this tutorial.</p>
Draft Genome Sequences of Two Bacteriocin-Producing Enterococcus faecium Strains Isolated from Nonfermented Animal Foods in Spain
<p>Raw sequences of two bacteriocin-producing Enterococcus faecium.</p> <p> </p>
Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterised by ITS-2 and COI sequences
<p class="MsoNormal"><span>Knowledge about parasite species of orcas, their prevalence and impact on the health status is scarce. Only two records of lungworm infections in orca exist from male neonatal orcas stranded in Germany and Norway. The nematodes were identified as <em>Halocercus</em> sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but morphological identification to species level remained impossible due to the fragile structure and ambiguous morphological features. Pseudaliid nematodes (Metastrongyloidea) are specific to the respiratory tract of toothed whales and are hypothesized to have become almost extinct in terrestrial mammals. Severe lungworm infections can cause secondary bacterial infections and bronchopneumonia and are a common cause of mortality in odontocetes. DNA isolations and subsequent sequencing of the rDNA ITS-2 and mtDNA COI revealed nucleotide differences between previously described <em>Halocercus</em> species from common dolphin (<em>H. delphini</em>) and harbour porpoises (<em>H. invaginatus</em>) that were comparatively analysed, pointing towards a potentially new species of pseudaliid lungworm in orcas. New COI sequences of six additional metastrongyloid lungworms of seals and porpoises were derived to elucidate phylogenetic relationships and differences between nine species of Metastrongyloidea.</span></p>
Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence
<p>Dataset for paper: Z. Qin, L. Wu, H. Sun, S. Huo, T. Ma, E. Lim, P.-Y. Chen, B. Marelli, M.J. Buehler, Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence, Extreme Mechanics Letters, Vol. 36, 100652, 2020. <a href="https://doi.org/10.1016/j.eml.2020.100652">https://doi.org/10.1016/j.eml.2020.100652</a>.</p> <p>Code: https://github.com/lamm-mit/MNNN/ </p>
sequenced cfDNA samples, extracted DoC for TSSs (HK + PAU) and TFBSs (LYL1 and GRHL2)
<p>File contains CSV files which store depth of coverage values (cfDNA fragment's central 60 bp if length > 60 bp; entire fragment otherwise) extracted from 4 samples (sample BAM files deposited at the European Genome Phenome Archive, accession: <span> </span><a href="https://ega-archive.org/studies/EGAS00001006963">EGAS00001006963</a><span><span>) before and after correction of sample specific GC sequence content bias (GC bias) by GCparagon software using a custom Pysam implementation. The Pysam implementation can read alignment tags for DoC computation which is required for the signal after bias correction.</span></span></p> <p><span><span>Extracted loci are top 10k reported transcription factor binding sites for LYL1 and GRHL2 as well as transcription start sites of housekeeping genes (HK genes) and unexpressed genes as assessed from the Protein atlas (PAU genes).<br> Pysam implementation by Kapidzic Faruk can be found here: </span></span><a href="https://github.com/Faruk-K/pysam">https://github.com/Faruk-K/pysam</a></p> <p>Linked to the <a href="https://github.com/BGSpiegl/GCparagon/tree/including_EGAS00001006963_results-DEV">GCparagon tool code repository</a> which is available on GitHub.</p> <p>For details see publication which is linked to the EGA dataset and the GitHub repository. (not published at moment of submission to Zenodo)</p>
A dataset for Customer Churn Prediction for Video Websites Incorporating Behavioral Sequence Features
<p>In order to study the issue of network customer churn, the iQiyi customer dataset was collected. Behavioral sequence features were extracted from it to build a deep learning model and experiments were conducted.Here, we provide the corresponding raw dataset, including all the data we used.</p>
DNA sequence data for two Roscoea species, R. stenophylla and R. australis (Zingiberaceae)
<p><span>This dataset includes three genomic regions, nrITS (ITS1-5.8S–ITS2) and two chloroplast DNA (cpDNA) regions (psbA-trnH and trnL-F) for two <em>Roscoea</em> species <em>R. stenophylla</em> and <em>R. australis</em> (Zingiberaceae).</span></p>
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing
<p>Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium <em>Halotia branconii</em> CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.</p>
Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence
<p>Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 Cterminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis.</p>
Regulation of T7 gp2.5 Binding Dynamics by its C-terminal tail, Template Conformation and Sequence
<p><sup>* </sup>To whom correspondence may be addressed: g.j.l.wuite@vu.nl<br> <sup># </sup>The first three authors should be regarded as joint first authors</p> <p><strong>Abstract</strong><br> Bacteriophage T7 single-stranded DNA-binding protein (gp2.5) binds to and protects transiently exposed regions of single-stranded DNA (ssDNA) while dynamically interacting with other proteins of the replication complex. We directly visualize fluorescently labelled T7 gp2.5 binding to ssDNA at the single-molecule level. Upon binding, T7 gp2.5 reduces the contour length of ssDNA by stacking nucleotides in a force-dependent manner, suggesting T7 gp2.5 suppresses the formation of secondary structure. Next, we investigate the binding dynamics of T7 gp2.5 and a deletion mutant lacking 21 C-terminal residues (gp2.5-Δ21C) under various template tensions. Our results show that the base sequence of the DNA molecule, ssDNA conformation induced by template tension, and the acidic terminal domain from T7 gp2.5 significantly impact on the DNA binding parameters of T7 gp2.5. Moreover, we uncover a unique template-catalyzed recycling behaviour of T7 gp2.5, resulting in an apparent cooperative binding to ssDNA, facilitating efficient spatial redistribution of T7 gp2.5 during the synthesis of successive Okazaki fragments. Overall, our findings reveal an efficient binding mechanism that prevents the formation of secondary structures by enabling T7 gp2.5 to rapidly rebind to nearby exposed ssDNA regions, during lagging strand DNA synthesis.</p> <p><strong>Data Set Description</strong><br> This data set contains the raw data and analysis code for the single-molecule study of the binding dynamics of T7 gp2.5 and its interactions with single-stranded DNA (ssDNA). The experiments utilized a custom-built setup combining dual optical trapping, confocal microscopy, and microfluidics.</p> <p><strong>Methodology</strong><br> The single-molecule experiments were performed at room temperature in a 5-channel microfluidic flow cell using a custom-built experimental setup that combines dual optical trapping, confocal microscopy, and microfluidics for single-molecule assays. Data analysis was conducted using Python, Origin, and MATLAB. Detailed methodology and instrument specifications are provided in the associated publication.</p> <p><strong>Data Set Structure</strong><br> - `Raw_Data/`: Contains raw data files in TDMS format.<br> - `Data_Analysis_Code/`: Contains the code used for data analysis and figure generation.</p> <p><strong>File Formats</strong><br> - Raw data files are in TDMS format.</p> <p><strong>Usage Notes</strong><br> Along with the raw data, we also provided the analysis code which generates the figures. Users should be aware of the required citations, license terms, and ethical considerations when using this data set.</p> <p><strong>Acknowledgments</strong><br> This work was financially supported by: ‘Crowd management: The physics of genome processing in complex environments’ of Stichting voor Fundamenteel Onderzoek der Materie, China Scholarship Council (funding No. 201704910912) and the European Union H2020 Marie-Sklowdowska Curie International Training Network AntiHelix, Grant Agreement n. 859853.</p> <p><strong>Author Contributions</strong><br> J.C-D., L X., M.T.J.H., and G.J.L.W. conceptualized the research; J.C-D., and L.X. collected data; I.H. built the combined optical trapping and confocal microscope instrument and developed the MATLAB code for the analysis of kymograph data; S.A.S. and A.v.O. provided purified wild type T7 gp2.5 and tested their biochemical activity; S-J L. provided purified gp2.5-Δ21C and tested their biochemical activity; L X. J.C-D., and M.T.J.H. analyzed the data; J.C-D., L X., M.T.J.H., and G.J.L.W. wrote the manuscript; G.J.L.W. supervised the project; the manuscript is read, revised and confirmed by all the<br> </p>
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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.