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2,271 results for “Next generation sequencing”
Next Generation sequencing and quantitative transcriptomic analysis in -77+/+ and -77-/- erythroid precursors
GEO Series GSE96059. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Data from: Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large dataset using next-generation sequence data
The utility of 18S and 26S in broad phylogenetic analyses has been much maligned due in large part to the low signal in both genes. However, few analyses have employed complete 26S rDNA sequences over a broad range of taxa, and most alignments of the two genes are done de novo, without taking into account the secondary structure of the two rRNA genes. Here we mine next-generation sequence data to compile large matrices (429 taxa) of complete 18S + 26S gene sequences, and we compare both de novo alignment methods with curated alignments done by eye that take into account secondary structure and hard-to-align regions (profile alignments). The combined 18S + 26S topology is overall very similar to recently published gene trees for the angiosperms based on three or more genes. Overall support for the backbone or framework of the combined tree is low (bootstrap support below 50%). Few major clades have bootstrap support above 50%. Most well-supported clades are tip clades (families and orders sensu APG III 2009). Importantly, the 18S + 26S rDNA topology is consistent with current estimates of relationships: the basalmost angiosperms are recovered (Amborellaceae, Nymphaeales, Austrobaileyales), as are most major clades, including Mesangiospermae, eudicots (Eudicotyledoneae sensu Cantino et al. 2007), core eudicots (Gunneridae sensu Cantino et al. 2007), rosids (Rosidae sensu Cantino et al. 2007), asterids (Asteridae sensu Cantino et al. 2007), and Caryophyllales. Most clades recognized at the ordinal level (sensu APG III 2009) are also recovered. However, there are also some unusual placements in the 18S + 26S topology, but none of these receives bootstrap support above 50%. The profile and de novo alignments gave very similar topologies. 18S + 26S trees remain useful sources of data in large combined analyses. This is the first time a large data set of complete 26S gene sequences has been employed at this scale; this gene in particular proved to be useful phylogenetically. Targeted sequencing of 18S/26S rDNA is not advocated here, but given that these regions provide useful phylogenetic information and are abundant in next-generation sequencing runs, we suggest that the data be used rather than discarded.
Figure 1 from: Shaoli M, Hao Y, Chao L, Yafu Z, Fuming S, Yuchao W (2018) The complete mitochondrial genome of Xizicus (Haploxizicus) maculatus revealed by next-generation sequencing and phylogenetic implication (Orthoptera, Meconematinae). ZooKeys 773: 57-67. https://doi.org/10.3897/zookeys.773.24156
Figure 1 Circular visualization of the mitogenome of Xizicus (Haploxizicus) maculatus.
Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations
Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.
Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.
A Prospective Study to Evaluate the Consistency of Next-Generation Sequencing(NGS)-Panels by Using Malignant Hydrothorax Form NSCLC
ClinicalTrials.gov study NCT03546452. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Next-generation Sequencing Technology in the Clinical Application of Respiratory Specimens
ClinicalTrials.gov study NCT07191080. IPD Sharing: NO. Countries: 1. Publications: 0.
Analysis of Deoxyribonucleic Acid and Ribonucleic Acid Next-Generation Sequencing in Non-Small Cell Lung Cancer Patients Without Pathological Complete Response Following Neoadjuvant Immunotherapy
ClinicalTrials.gov study NCT07179445. IPD Sharing: NO. Countries: 1. Publications: 0.
Swallowable Sponge Cell Sampling Device and Next Generation Sequencing in Detecting Esophageal Cancer in Patients With Low or High Grade Dysplasia, Barrett Esophagus, or Gastroesophageal Reflux Diseas
ClinicalTrials.gov study NCT02890979. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Early Assessment of Lymphoma Treatment Response Using Phased Variant Analysis With Next-Generation Sequencing
ClinicalTrials.gov study NCT06550427. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Clinical Value of Next Generation Sequencing in Endocrine Therapy for Advanced Hormone Receptor Positive/HER-2 Negative Breast Cancer
ClinicalTrials.gov study NCT03786575. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Rapid Genetic Diagnosis Employing Next Generation Sequencing for Critical Illness in Infants and Children
ClinicalTrials.gov study NCT03175692. IPD Sharing: NO. Countries: 1. Publications: 0.
Metagenomic Next-Generation Sequencing for Diagnosis of Ascites Infection in End-stage Liver Diseases
ClinicalTrials.gov study NCT04125654. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Next Generation Sequencing（NGS）Monitors Minimal Residual Disease（MRD）in Allo-PBSCT Patients
ClinicalTrials.gov study NCT04126967. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Utility of Next-generation Sequencing for the Diagnosis of Periprosthetic Joint Infection
ClinicalTrials.gov study NCT03200470. IPD Sharing: Not stated. Countries: 1. Publications: 0.
EBUS-TBNA vs Transbronchial Mediastinal Cryobiopsy for Adequacy of Next Generation Sequencing
ClinicalTrials.gov study NCT06105801. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Transcriptomic and Next Generation Sequencing Approaches to Infection With Treponema Pallidum
ClinicalTrials.gov study NCT03310424. IPD Sharing: YES. Countries: 1. Publications: 0.
A Relevance Study Between the Result of Clinical Drug Intervention and Next-generation Sequencing Technology Focused on Refractory Helicobacter Pylori Infection
ClinicalTrials.gov study NCT02806674. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Next Generation Sequence Target-Directed Therapy in Treating Patients With Cancer
ClinicalTrials.gov study NCT02132845. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Improving Genetic Counseling for Patients With Spina Bifida Using Next Generation Sequencing
ClinicalTrials.gov study NCT02854150. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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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.