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595 results for “High-throughput sequencing”
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data
<p>The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has limited the ability to identify major morphological and biogeographic transitions. We used target capture sequencing with the Angiosperms353 kit for over 300 species across Ericales, tree-based sequence curation, and multiple phylogenetic approaches to investigate the phylogenetics of the major clades of Primulaceae and their relationship to other Ericales. The study included 150 samples of Primulaceae comprising nearly all recognized genera of the family, with a particular focus on the most diverse subfamily, Myrsinoideae, for which previous phylogenetic knowledge was poor. We used fossil and secondary calibrations to generate dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as ancestral state reconstructions of plant habit.</p>
Characterizing the diet of a threatened seabird, the Marbled Murrelet (Brachyramphus marmoratus), using high-throughput sequencing
<p class="blockindent">Understanding prey consumption patterns is critical to understanding the ways in which seabirds cope with a changing ocean. However, characterizing the dietary habitats of seabirds can be challenging. In this study, we investigated the diet of the Marbled Murrelet (<span class="bodyitalic"><em>Brachyramphus marmoratus</em>) </span>population that lives in waters off California, Oregon, and Washington, USA, using fecal DNA, custom metabarcoding, and high-throughput sequencing. Murrelets were captured at sea by dip-netting at night. Across this region, murrelets consumed highly diverse prey types including 17 fish species and 10 invertebrate species, in accord with previous work indicating the species' forage on a wide range of prey. Pacific Herring (<em><span class="bodyitalic">Clupea pallasii</span></em><span class="bodyitalic">)</span> was the most common prey in Washington and Oregon (frequency of occurrence = 0.84 and 0.69, respectively), replaced by Northern Anchovy <span class="bodyitalic">(Engraulis <em>mordax</em>) </span>in California (frequency of occurrence = 0.77). In Oregon, where our sample size was sufficient, diet composition differed between the 2017 and 2018 breeding seasons, with an apparent decline in the proportional consumption of energy-dense prey. Common and energy-dense prey were consumed in equal proportions by males and females, perhaps because of foraging in the same habitat. Diet did not vary between breeders and non-breeders. Our study offers the first detailed report on the diet of adult Marbled Murrelets in waters where they are listed as Threatened by the US federal government. This indicates that managing fisheries and conserving spawning habitat for high-occurrence prey species could benefit murrelet populations.</p>
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data
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Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications
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Data from: High-throughput mRNA sequencing-based DEGs: HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype
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Characterizing the diet of a threatened seabird, the Marbled Murrelet (Brachyramphus marmoratus), using high-throughput sequencing
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Data from: High-throughput sequencing of nematode communities from total soil DNA extractions
Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDNA
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Supplementary material 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Common OTU lists and Statistical analysis : Explanation note: This file contains detected OTUs in both methods and biodiversity analysis (GLM and t-test)
Supplementary material 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Biodiversity workflow in R : Explanation note: Bundle of files for biodiversity analysis in R. All necessary input files and a commented script of R-commands are provided.
Supplementary material 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Master data sheet : Explanation note: Spreadsheet file containing information about read abundances of operational taxonomic units (OTUs) and sample metadata. Here, data were prepared for subsequent biodiversity analysis in R.
Supplementary material 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Bioinformatics pipeline : Explanation note: This file provides all steps and commands necessary for quality filtering and demultiplexing of raw paired fastq sequences.
Supplementary material 1 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing. Metabarcoding and Metagenomics 1: e13709. https://doi.org/10.3897/mbmg.1.13709
OSR aphid mummy collection. Sampling location and size / Amplification success of mummies' DNA extracts by Illumina sequencing.
Bacterial cell surface characterization by phage display coupled to high-throughput sequencing
<p>This record contains the processed high-throughput sequencing data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Data was generated using the <a href="https://github.com/caseygrun/phage-seq">Snakemake workflows and Jupyter notebooks in this repository</a> and is intended to be analyzed further using the notebooks in that repository</p> <p>Each tarball within this record, when expanded, populates the <code>results</code> and <code>intermediate</code> directories of one of those workflows: <code>alpaca-library</code> ,<code>panning-small</code>, <code>panning-massive</code>, or <code>panning-extended</code>. Clone the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>, then download one or more of these tarballs to the corresponding directory of that directory. For example:</p> <blockquote> <pre><code>git clone https://github.com/caseygrun/phage-seq.git cd panning-extended wget https://zenodo.org/records/11246658/files/panning-extended-results.tar.gz tar vzxf panning-extended-results.tar.gz</code></pre> </blockquote> <p>More detailed instructions are included in the README for the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>.</p>
Supplementary material 9 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Bland-Altman plots for the total fish eDNA (a), Japanese anchovy (Engraulis japonicus; b) and Japanese jack mackerel (Trachurus japonicus; c). Dashed lines indicate 95% uppper and lower limits and solid line indicates mean value.
Supplementary material 6 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The numbers of eDNA copies of marine fish species quantified by metabarcoding with the internal standard DNA
Supplementary material 8 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and DNA copy numbers quantified by qPCR. Correlations for the total fish eDNA (all data, a; enlarged figure, b), Japanese anchovy (Engraulis japonicus; all data, c; enlarged figure, d) and Japanese jack mackerel (Trachurus japonicus; all data, e; enlarged figure, f). Dashed and soild lines indicate 1:1 line and linear regression line, respectively. Regression lines in the enlarged figures were drawn by excluding outliers. All regression lines, except for the lines for total fish eDNA, were significant (P < 0.05). Dotted boxed regions in a, c and e correspond to the range of the graphs in b, d and f, respectively. The intensity of red colour indicates the slope of the regression line used to convert sequence reads to the copy numbers.
Supplementary material 4 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and copy numbers of standard DNAs for 52 samples. Blue line indicates the linear regression between sequence reads and copy numbers. The regression lines are used to convert the MiSeq reads into the calculated copy numbers. Numbers in a grey region indicate sampling date. Note that regression slopes are different amongst samples, i.e. the number of sequence reads generated per eDNA copy is different amongst samples.
Supplementary material 5 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between regression residuals and copy numbers of standard DNAs for 52 samples. Dashed line indicates zero residuals.
Fig. 3 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Fig. 3 Correlation between the samples positions obtained on the first axes of the PCA based on microscopy and HTS diatom composition of the samples. There is a highly significant correlation (p <0.001, R 2 = 31%) between both axes
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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)
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.