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78 results for “ngs sequencing”
Raw NGS data for the study 'Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing'
<p>This file contains the original next-generation sequencing data (raw sequences in fastq format) which were analyzed in the study titled: "Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing".</p> <p> </p> <p> </p>
Raw sequencing data of NGS of stomach contents of sympatric species of weakly electric fish (genus: Campylomormyrus)
<p>This dataset contains the raw sequencing data of stomach contents of sympatric species of weakly electric fish (genus: <em>Campylomormyrus</em>) using next generation sequencing.</p> <p>Stomach content samples were collected from five <em>Campylomormyrus</em> species (<em>C. alces</em>, ; <em>C. compressirostris</em>, ; <em>C. curvirostris</em>, ; <em>C. numenius</em>, ; <em>C. tshokwe</em>) and samples of <em>Gnathonemus petersii</em> (<em>G. petersii, </em>), a sister genus of <em>Campylomormyrus.</em></p> <p>The fish specimens, from which these stomach content samples are extracted, were collected during an expedition to the Republic of the Congo in fall 2012.</p> <p>The dataset files are in FASTA format.</p>
Original NGS dataset from publication "Next-generation sequencing analysis of a cluster of hepatitis C virus infections in a haematology and oncology center".
<p>Original hepatitis C virus hypervariable region 1 NGS sequences in fastq format from patients analyzed in the study "Next-generation sequencing analysis of a cluster of hepatitis C virus infections in a haematology and oncology center". </p> <p> </p>
Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
<p>These data are the DNA sequences obtained from samples of house plaster with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the wall were sampled. the DNA was extracted using the Spin Kit For Soil MPBio. </p> <p>The DNA extracts were sequenced by NGS using Illumina MiSeq</p> <p>Two regions were selected V3V5 16S for Bacteria and ITS1 ITS for Fungi. </p>
Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas
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Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages
Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.
FIGURE 2 in USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS
FIGURE 2. Relative abundances of reads of fungal genera per study area and metabarcode using 95% sequence similarity with reference sequences in the UNITE database as surrogate for traditional taxonomic generic concepts.
FIGURE 1 in USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS
FIGURE 1. Genera richness at the levels of phylum, class and order per study area and metabarcode using 95% sequence similarity with reference sequences in the UNITE database as surrogate for traditional taxonomic generic concepts.
SARA module 3: NGS epitope sequencing: Illumina FASTQ files
<p>We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.</p>
Research on the Heterogeneity of Taiwanese Breast Cancer Patients by Next Generation Sequencing (NGS) Tools
ClinicalTrials.gov study NCT04626440. IPD Sharing: NO. Countries: 1. Publications: 1.
Prospective Clinical Validation of Next Generation Sequencing (NGS) and Patient-Derived Tumor Organoids (PDO) Guided Therapy in Patients with Advanced/ Inoperable Solid Tumors
ClinicalTrials.gov study NCT06077591. IPD Sharing: NO. Countries: 1. Publications: 11.
Development of a Next Generation Sequencing (NGS) -Based Assay to Detect Preeclampsia Molecular Markers
ClinicalTrials.gov study NCT02808494. IPD Sharing: NO. Countries: 1. Publications: 1.
Prognostic Values of Next Generation Sequencing (NGS) in Acute Myeloid Leukemia Patients With Allo-HSCT
ClinicalTrials.gov study NCT03715621. IPD Sharing: UNDECIDED. Countries: 1. Publications: 25.
Assessment of Urinary Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS) Technology in the Evaluation and Management of Females With Chronic Bladder Pain and Cystitis-like Symptoms
ClinicalTrials.gov study NCT05276466. IPD Sharing: NO. Countries: 1. Publications: 6.
Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
ClinicalTrials.gov study NCT05581160. IPD Sharing: NO. Countries: 1. Publications: 18.
A Prospective Cohort of Obinutuzumab and Chlorambucil (GC) Chemotherapy for the Treatment of Elderly Patients With Chronic Lymphocytic Leukemia Including Next- Generation Sequencing (NGS)-Based Assess
ClinicalTrials.gov study NCT04059081. IPD Sharing: UNDECIDED. Countries: 1. Publications: 9.
Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages
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SARA module 3: NGS epitope sequencing: Illumina FASTQ files
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Data from: "NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
Introduction: The gypsy moth, Lymantria dispar, and the nun moth, Lymantria monacha, are closely related species (Lepidoptera, Lymantriidae), co-seasonal and economically important forest pests on broadleaf and coniferous trees. In Central Europe, gypsy moth larvae are frequently parasitized by the gregarious, endoparasitic wasp Glyptapanteles liparidis (Hymenoptera, Braconidae). At oviposition, the female wasp injects between 10 and up to 100 eggs into the hemocoel of a single host larva, together with venom and calyx fluid containing polydnavirus (PDV) particles that subsequently play a critical role in suppressing the host immune response so that successful development of the parasitoid can proceed (Schopf 2007). These viruses, which are integrated in the genomic DNA of the wasp and undergo replication only in the female's ovary, rapidly enter host hemocytes, fat body, and nervous system following parasitization, and viral genes are expressed. In L. dispar larvae parasitized by G. liparidis, the host's hemocytes alter their behavior, fail to spread properly (thereby inhibiting the encapsulation response) and partly undergo programmed cell death (apoptosis), resulting in a dramatic drop in the host's total hemocyte number (Schafellner and Schläger 2009).
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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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.