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590 results for “targeted sequencing”
Comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity using Oxford Nanopore sequencing
<p><span>Metagenomics has become a prominent technology for studying the functional potential of all organisms in a microbial and eukaryotic community. The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. To achieve this, we have developed a universal PCR assay that targets the most conservative nuclear regions of the ribosomal gene for all cellular organisms, including plants, algae, fungi, protists, insects</span>,<span> and animals. The amplification product contains polymorphic regions of both ribosomal genes and the intergenic spacer. The size of the PCR products varies by class, kingdom</span>,<span> or domain, ranging from 2 kb for fungi to 7 kb for birds. This assay is also adapted for use with the Oxford Nanopore Rapid Barcoding Library Kit, which enables metagenomic biodiversity analysis. Our approach provides a rapid, sensitive</span>,<span> and equally efficient way to study the composition of eDNA from mixed species in the environment. This protocol reduces the time and cost of metagenomic biodiversity analysis using Oxford Nanopore sequencing. We can efficiently analyze the biodiversity of mixed species present in environmental samples.</span></span></p>
Oxford Nanopore sequencing for comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity
<p><span>The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here, we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. </span></span></p>
Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina
<p>Background: Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.</p> <p>Results: We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via <em>Agrobacterium</em>. We present an example using the allohexaploid oil-seed plant <em>Camelina sativa</em> to determine insertion site location of two transgenes.</p> <p>Conclusion: This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.</p>
Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data
<p><span>The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.</span></p>
Data in support of Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica
<p>Includes alignments and trees for the analysis found in Thomas et al. 2021, Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica; American Journal of Botany, Special Issue: Exploring Angiosperms353: a Universal Toolkit for Flowering Plant Phylogenomics. Alignments comprise subsets of Angiosperms353 genes given each filtering scheme (full, intersection, sortadate_BP, sortadate_TL) and gene type/subset (exons, introns, supercontigs), and for markers downloaded from GenBank, as explained in the Methods section of Thomas et al. 2021. Trees were included for each of these alignments from IQtree and Astral; SVDquartets tree was only estimated for the full set of supercontigs. Gene trees were generated with IQtree. Tree files are named differently than the final manuscript; refer to the number of genes specified in Fig 1 of Thomas et al, 2021 and specified in each filename to identify filtering scheme. Raw sequence reads are available on the Sequence Read Archive at <a href="http://www.ncbi.nlm.nih.gov/bioproject/715342">http://www.ncbi.nlm.nih.gov/bioproject/715342</a>.</p>
Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits
<p><strong>Premise:</strong> Both universal and family-specific targeted sequencing probe kits are becoming widely used for the reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships.</p> <p><strong>Methods:</strong> We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit, and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support.</p> <p><strong>Results:</strong> For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. The merging of data obtained with the two kits resulted in a well-supported phylogenetic tree.</p> <p><strong>Conclusions:</strong> The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family-specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.</p>
Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
<p>"Mid-density" targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTag<sup>TM</sup> technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium<sup>TM</sup> SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher-density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.</p>
Nucleotide sequence database of Copper-containing membrane monooxygenases genes for analysing primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia oxidising Nitrospira
<p>Nucleotide sequences of 487 Cu-mmo genes, including amoA comammox clade A and clade B, amoA ammonia oxidizing bacteria as well as other Cu-mmo genes.</p>
Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
<p>Data from study, protocol published at 10.5281/zenodo.5081880</p> <p><strong>Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. </strong>(BAL: bronchoalveolar lavage.) *Not included in validation numbers as duplicate at sub-species or genus level detection, **MecA was not included in validation numbers. TAC hits which did not pass the internal quality control standards required for reporting are indicated by (not reported). Samples which did not undergo sequencing indicated by <em>ND</em>. (✓) indicates low confidence hits from sequencing.</p>
B-other ALL classification by Targeted RNA-sequencing
<p>We present a comprehensive genetic study of 144 pediatric B-other Acute Lymphoblastic Leukemia cases diagnosed and treated at Boldrini Children's Hospital (Brazil). We performed a targeted RNA-sequencing to evaluated the benefits of introducing genomic technologies into routine diagnostics. Targeted RNA-sequencing further classified 66.7% B-other cases. All 'classical' and novel ALL subgroups, except for iAMP21, hyper- and hypodiploid cases were identified. In addition, clinically important genetic alterations as druggable lesions and prognostic factors were found. Here, we uploaded files that contain: </p> <p>1. Gene expression data from the entire cohort studied, n=184 (Log2+1 TPM normalized gene expression data). Tab-delimited file (.csv) that contains a row for gene, a column for each sample, and expression values for each gene in each sample. Annotation labels are in the first three rows and in the first column.</p> <p>2. A subset of 23 BAM (Binary Alignment/Map) files for representative ALL cases, including BCR-ABL1, ETV6-RUNX1, TCF3-PBX1, KMT2A-r, High-Hyperdiploidy; DUX4-r, iAMP21, PAX5-driven, ABL-class fusion, JAK2-fusion, EPOR-fusion, CRLF2-high, ZNF384-r, MEF2D-r, NUTM1-r, B-'rest', IKZF1del, and ERGdel.</p> <p>3- Genetic information of the 23 BAM files provided (tab-delimited file, .txt). </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>
Sequences of target genes and probes for construction of exon-targeted libraries for Prunus spp.
<p>(Files)</p> <p>"baits-selection-15171.fas": Sequences of 15,171 baits used for hybridization reaction.</p> <p>"Targets_mume.15171.xlsx": Sequences of target genes used for design baits.</p> <p> </p> <p>(Protocol for bait design)</p> <p>To selectively retrieve libraries with exons, a myBaits Custom design kit was used to design 1–20-K probes (Arbor Biosciences, Ann Arbor, MI, USA), which uses biotinylated RNA probes to concentrate fragments carrying sequences of interest (Gnirke et al., 2009), based on the published genomic and coding sequences of <em>P. mume</em> (Zhang et al., 2012). We subjected 29,621 non-redundant coding loci to search for single hits with BLAST+ (MEGABLAST with -p 70) against the <em>P. mume</em> genome, for the subsequent bait design. A 120-mer bait with 25–55 GC% per locus was randomly designed for each locus, and finally we obtained a bait set targeting 15,171 coding loci.</p>
Raw target enrichment of conserved element sequence data for 24 black coral species
<p><span>Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of "source" slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection. </span></p>
Effect of a Sequence of Specific Manual Therapy Techniques Targeting the Autonomic Nervous System in Healthy Adults
ClinicalTrials.gov study NCT06477822. IPD Sharing: NO. Countries: 1. Publications: 18.
Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data
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Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits
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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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Development and application of Faba_bean_130K Targeted Next-Generation Sequencing SNP genotyping platform based on transcriptome sequencing
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Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
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Raw target enrichment of conserved element sequence data for 24 black coral species
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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)
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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.