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4,566 results for “marker”
Figure 1 in Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach
Figure 1. Backcrossing program used in this study to develop improved lines of rice (BC F ).
Exploring ultraweak photon emissions as optical markers of brain activity - Dataset and statistical models
Open the record for dataset details and reuse information.
Supplemental Table 1- Marker-Gene-List
<p>Supplementary data to a mauscript titled </p> <p><span>Gonadotropin releasing hormone - gonadotropes interactions revealed by pituitary single-cell transcriptomics in zebrafish</span></p>
Avian influenza markers
<p><span>The spreadsheets summarizing the identified AIV zoonotic markers </span></p>
Bucket Table Edwards et al 2021 Metabolomic Markers of Storage Temperature and Time in Pasteurized Milk
<p>NMR spectroscopic data of a set of milk samples at different temperatures and storage times. Spectra were binned using AMIX 3.9.15 (Bruker BioSpin, Rheinstetten, Germany).</p>
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
<p>The study used genetic mapping and coverage data in genome sequences of multiple male and female individuals of <i>M. picta</i> from multiple natural populations to investigate genetic degeneration of the Y chromosome, and quantify gene loss from the Y. The files include coverage results from the sex chromosome that were (i) used for sexing the sequenced individuals, and (ii) combined with autosomal results to analyze M/F, M/A and F/A depth of coverage ratios. Genetic mapping was also used to validate sex linkage, and the data set includes files with genotypes of genetic markers.</p>
DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
<p>DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome <i>c</i> oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed "universal" markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macro-eukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image-based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multi-marker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.</p>
Protocols for marker-free gene knock-out and knock-down in Kluyveromyces marxianus using CRISPR/Cas9
<p>This file contains the CRISPR targets predicted for every gene in the NBRC1777 genome, you can use it to design primers to target the gene you are interested in. There is one folder per gene. The 'sgRNAcas9_report' file contains a list of all the predicted sites, their position in the gene, and other extra information (e.g. GC content, off targets, etc..). The 'TargetSeq.fa' file contains the sequence of the gene targeted. For more information see <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100448">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100448</a></p>
Juniperus excelsa s. str. in Crimea – differentiation and history inferred from genetic and morphological markers
<p>The file contains Supplementary Data for the paper: Mazur M., Jadwiszczak KA., Bona A., Krasylenko Y., Kukushkin O., Marcysiak K. 2021.<em> Juniperus excelsa</em> s. str. in crimea – differentiation and history inferred from genetic and morphological markers. Folia Forestalia Polonica, vol.63, no.4, pp.276-288. <a href="https://doi.org/10.2478/ffp-2021-0028">https://doi.org/10.2478/ffp-2021-0028</a></p>
Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat
<p>The study material in the GWAS panel with 193 bread wheat genotypes from Indian and exotic collections was selected to map the genomic regions responsible for grain iron and Zinc content under drought and heat stress treatments.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR), Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on Grain Iron and Grain zinc content along with thousand-grain weight. Around 20 g of grain sample from each of 282 genotypes from the GWAS panel under all three conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >10%, and heterozygote frequency >50% were removed from the analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS analysis.</p>
Second-line drug resistance markers as proxy indicators of sputum culture conversion for samples tested in Uganda
<p>Increased TB disease burden arises as a result of low treatment success rates stemming from the emergence of second-line drug (SLD) resistance. We aimed at determining the usefulness of SLD resistance markers as proxy indicators of time to sputum culture conversion; a renowned predictor of Tuberculosis (TB) treatment outcome, among SLD-resistant TB patients tested at the Uganda National TB Reference Laboratory (NTRL). A cross-sectional study was conducted on 72 bacteriologically confirmed SLDR TB patients with datasets including culture conversion time and second-line probe assay mutation profiles between 01/06/2017 and 31/12/2019. The data were then imported into STATA v15 for descriptive statistical analysis, Univariate cox proportional hazard model analysis and Kaplan-Meier survival curves at a 5% level of significance; p-value ≤ 0.05. Results indicate the median time was achieved at 3 (0–12) months across the studied patients. The <em>rrs</em> G1484T mutation associated with conferring drug resistance to aminoglycosides was observed to have the shortest median conversion time of 1.5 months and the longest by the <em>gryB</em> E540D at 5 months. A single mutation in the <em>gryA</em> gene locus showed higher converted proportions 70.8% (58.9–81.0) than those that had two 8.3% (3.1–17.3) or three 2.7% (0.3–10.0) mutations. We conclude that the studied second-line drug resistance markers had no statistically significant association with the time to sputum culture conversion, although increased drug resistance levels reduced the converted proportions and stressed the need to utilize molecular diagnostics data to better comprehend proxy indicators of SLD-resistant tuberculosis management.</p>
A common resequencing‐based genetic marker dataset for global maize diversity
<p>Maize (<em>Zea mays ssp. mays</em>) populations exhibit vast amounts of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies, and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here we employ resequencing data from 1,276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of ~366 million segregating variants and ~46 million high confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering time genes using previously published trait datasets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.</p>
A range-wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence
<p><strong><span>Aim: </span></strong><span>Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming.<strong> </strong>We infer the hitherto unresolved postglacial history of <em>Pinus cembra.</em> Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re-colonisation routes.</span></p> <p><strong><span>Location: </span></strong><span>European Alps and Carpathians.</span></p> <p><strong><span>Taxa: </span></strong><em><span>Pinus cembra.</span></em></p> <p><strong><span>Methods: </span></strong><span>We genotyped nuclear and chloroplast microsatellite markers in nearly 3,000 individuals from 147 locations across the entire natural range of <em>P. cembra</em>. Spatial genetic structure (Bayesian modelling) and demographic history (Approximate Bayesian Computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re-colonisation of the current range.</span></p> <p><strong><span>Results: </span></strong><span>We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial <em>c.</em> 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during post-glacial re-colonisation.</span></p> <p><strong><span>Main conclusions: </span></strong><span>Combining genetic and palaeoecological evidence suggests that <em>P. cembra</em> primarily survived the LGM in "cold period" refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene "warm period" refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographic break in the European Alps also found in herbaceous alpine plant species.</span></p>
Origins of green turtle fishery bycatch in the Central Pacific revealed by mixed genetic markers
<p>Longline fishing vessels, such as those that target tuna or billfish, also unintentionally catch endangered marine turtle species on the high seas. The stock composition of this bycatch is often unknown but potentially complex, with individuals coming from many possible origins on an ocean-basin scale. To better understand the stock composition of green turtle (<em>Chelonia</em> <em>mydas</em>) bycatch, we obtained 46 turtles, 27–78 cm in curved carapace length, caught by Hawaii- and American Samoa-based pelagic longline fishing vessels across large areas of the North- and South-central Pacific. We genotyped these at nine microsatellite loci and one mitochondrial DNA marker and used a baseline of 1,043 nesting female green turtles from beaches across the Pacific for population assignment and mixed-stock analysis. By analyzing both marker types jointly we were able to increase power and genetically resolve ten baseline stocks of nesting females with mean self-assignment and simulated accuracies of 75–97%. Above the Equator, green turtle bycatch was composed mostly of individuals from Hawaiian and Eastern Pacific stocks, with a small number from the Western Pacific. Below the Equator, the most common stocks in the bycatch were from Australia and the Coral Sea, American Samoa and French Polynesia, and the Galápagos Islands. Overall, turtles originating from East, West, and Central Pacific breeding populations were major components of the bycatch, suggesting that the geographic ranges of these populations overlap across large tracts of ocean during the pelagic life history stages.</p>
ANION GAP OR SERUM LACTATE-IN SEARCH OF A BETTER PROGNOSTIC MARKER IN SEPSIS A CROSS-SECTIONAL STUDY IN A RURAL TERTIARY CARE HOSPITAL
<p>master data sheet</p>
Key files for: Comparative genomic analysis of Microcystis strain diversity using conserved marker genes
<p>Key data outputs to accompany the manuscript "Comparative genomic analysis of Microcystis strain diversity using conserved marker genes"</p>
Data from: Compensatory growth is accompanied by changes in insulin-like growth factor-1 but not markers of cellular aging in a long-lived seabird
<p>Developing organisms often plastically modify growth in response to environmental circumstances, which may be adaptive, but is expected to entail long-term costs. However, the mechanisms that mediate these growth adjustments and any associated costs are less well understood. In vertebrates, one mechanism that may be important in this context is the highly conserved signaling factor insulin-like growth factor-1 (IGF-1), which is often positively related to post-natal growth and negatively related to longevity. To test this idea, we exposed captive Franklin's gulls (<em>Leucophaeus</em> <em>pipixcan</em>) to a physiologically relevant nutritional stressor by restricting food availability during post-natal development and examined the effects on growth, IGF-1, and two potential biomarkers of cellular and organismal aging (oxidative stress, and telomeres). During food restriction, experimental chicks gained body mass more slowly and had lower IGF-1 levels than controls. Following the food restriction, experimental chicks underwent compensatory growth, which was accompanied by an increase in IGF-1 levels. Interestingly however, there were no significant effects of the experimental treatment or of variation in IGF-1 levels on oxidative stress or telomeres. These findings suggest that IGF-1 is responsive to changes in resource availability but is not associated with increased markers of cellular aging during development in this relatively long-lived species.</p>
Phylomitogenomics reveals mito-nuclear concordance in social wasps: the performance of mitochondrial markers and gene order for hymenopteran systematics.
<p>Mitochondrial (mtDNA) genes have served as widely utilized genetic loci for animal phylogenetics and phylogeography studies. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analyzed mitogenomic data from social wasps, representing the four recognized tribes of Polistinae and also all Epiponini genera. Additionally, we evaluated whether mtDNA gene order in Polistinae is congruent with its tribal classification. Using concatenation phylogenetic methods, we show phylogenetic congruence between mitogenomic and nuclear data. Statistically comparing the phylogenetic performance of individual mtDNA genes, we demonstrate that for social wasps the molecular markers COI, 16S, NAD5, and NAD2 perform best, while ATP6, COII, and 12S show the worst results. Finally, we verified that the tRNA cluster close to the noncoding region is a hotspot of rearrangement in Vespidae and can be used as additional information for the systematics of this group. Together, these results indicate that mitogenomes contain robust phylogenetic signal to elucidate the evolutionary history of Vespidae. Moreover, our study identifies the best choice of mitochondrial markers for systematic investigations of social wasps.</p>
Absolute time markers and age-depth model for the last 75 kyr of Lake Chala sediments
<p>The 171 time markers include 162 <sup>14</sup>C ages on bulk organic matter or grass charcoal in sediment intervals of the composite Challacea (CH03, CH05) sequence (Blaauw et al., 2011), transferred to the DeepCHALLA (DCH) composite sequence using mm- or cm-scale cross-correlation of visual lithostratigraphy (Baxter et al., 2023). The other nine time markers are six <sup>210</sup>Pb-dated intervals from gravity core CH99-1G transferred to the CH05 and DCH sequences using 1-cm resolution magnetic-susceptibility profiles (Blaauw et al., 2011), the November 2016 (DCH) and March 2005 (CH05) sediment-water interfaces, and the YTT cryptotephra (Baxter et al., 2023). Lab codes stand for the Poznan Radiocarbon Laboratory (Poz-), the Chrono Centre at Queen’s University in Belfast (UBA-), the Isotope Physics Laboratory at the University of Groningen (GrA-), the Saint-Croix Watershed Research Station of the Science Museum of Minnesota (SMM), and the Cambridge Tephra Laboratory (CT-). ‘Offset’ refers to the old-carbon age offset of bulk organic <sup>14</sup>C dates, modelled using 16 paired dates on bulk organic matter and grass charcoal and three sections allowing <sup>14</sup>C wiggle-match dating using closely spaced bulk organic samples (Blaauw et al., 2011). The compound error on corrected <sup>14</sup>C ages was calculated as SQRT ((Age Error)^2 + (Offset STD)^2). All dated intervals are represented by their DCH event-free depth in meter (mefd). </p>
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.