Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Real-time species typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

ABSTRACT: Real-time species typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

PROVIDER: PRJEB11687 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Real-time species typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

Project description:Real-time species typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

| PRJEB14532 | ENA

Oxford Nanopore MinION sequencing of multiplex PCR amplified, pathogen-spiked blood and plasma samples

Project description:To evaluate targeted MinION next generation sequencing as a diagnostic method for detection of pathogens in human blood and plasma, human blood or plasma samples were spiked with measured amounts of viruses, bacteria, protozoan parasites or tested pathogen-free as negative controls. Nucleic acid was extracted from samples and PCR amplification performed in multiplex primer pools with a procedure described in ArrayExpress experiment submission ID 18379. The PCR products were used for library preparation. The libraries sequenced on an Oxford Nanopore MinION. The passed reads aligned with a custom reference file to determine the identity of the pathogen in the sample.

2024-06-08 | E-MTAB-14011 | biostudies-arrayexpress

Oxford Nanopore RNA sequencing for HLA typing

Project description:A targeted RNA-based method for typing of 12 classical HLA genes using Oxford Nanopore sequencing. In the method, were enriched HLA genes from cDNA of 50 individuals using gene-specific reverse primers. The library molecules were then barcoded, pooled into 2 separate gene pools, and sequenced on MinION R9.4 SpotON flow cells.

| EGAS00001004918 | EGA

MinION nanopore sequencer performance analysis

Project description:A reference dataset for phage M13 dsDNA generated with the Oxford Nanopore MinION

| PRJEB8318 | ENA

MinION Nanopore Sequencing for Influenza A Viruses

Project description:Rapid Multiplex MinION Nanopore Sequencing Workflow for Influenza A Viruses

| PRJEB35098 | ENA

MinION Influenza

Project description:MinION nanopore sequencing of an influenza genome

| PRJEB9812 | ENA

Solanum americanum clone 954750186 Nanopore MinION RenSeq

Project description:Oxford Nanopore MinION resistance-gene enrichment sequencing of Solanum americanum clone 954750186

| PRJEB18993 | ENA

MinION DNA Sequencing

Project description:Improved data analysis for the MinION nanopore sequencer

| PRJEB8230 | ENA

The microprotein Minion controls cell fusion and muscle formation

Project description:These findings establish minion as a novel microprotein required for muscle development, and define a two-component program for the induction of mammalian cell fusion.

2017-05-19 | GSE97764 | GEO

Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples.

Project description:Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer's instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples.

| S-EPMC7201198 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data