Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human pathogens

ABSTRACT: Metagenomic sequencing for neuropathological diagnosis of infections of the nervous system

PROVIDER: PRJNA314149 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3214090.fastq.gz	Fastqsanger.gz
	SRR3214091.fastq.gz	Fastqsanger.gz
	SRR3214092.fastq.gz	Fastqsanger.gz
	SRR3214093.fastq.gz	Fastqsanger.gz
	SRR3214094.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

human gut metagenome

Project description:Metagenomic diagnosis of viral infections - RAPID project

| PRJNA33495 | ENA

Project description:7-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections

| PRJNA1143941 | ENA

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.

2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress

Effect of antivirals in NPCs derived from induced pluripotent stem cells

Project description:Neurotropic viral infections of the central nervous system (CNS) cause a broad spectrum of clinical manifestations, which include neuropathological changes and subsequent neurological conditions. Currently utilized antiviral drugs are targeted towards specific viruses or members of a specific family. However, the recent COVID-19 pandemic caused by the neurotropic virus SARS-CoV-2 has highlighted the importance of having broad spectrum agents available in our armamentarium that can limit replication of emerging and reemerging neurotropic viruses and future unidentified pathogens that can pose a risk for the next pandemic. Neural progenitor cells (NPCs) were derived from hiPSC-neurons as previously described (D’Aiuto et al. Organogenesis. 2014;10(4):365-77).

2023-05-01 | GSE201156 | GEO

human metagenome

Project description:Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis

| PRJNA298217 | ENA

CNS mNGS

Project description:Central nervous system infection diagnosed by metagenomic next-generation sequencing

| PRJEB48018 | ENA

Project description:Diagnosis and Surveillance of Neonatal Infections by Metagenomic Next-Generation Sequencing

| PRJNA808819 | ENA

Single-nucleus transcriptomic profiles of glial cells in human dorsal root ganglion and spinal cord

Project description:Glial cells are present throughout the entire nervous system and paly a crucial role in regulating physiological and pathological functions, such as infections, acute injuries and chronic neurodegenerative disorders. The glial cells mainly include astrocytes, microglia, and oligodendrocytes in the central nervous system (CNS), and satellite glial cells (SGCs) in the peripheral nervous system (PNS). Although the glial subtypes and functional heterogeneity is relatively well understood in mice by recent studies using single-cell or single-nucleus RNA-sequencing, no evidence yet has elucidate the transcriptomic profiles of glia cells in PNS and CNS. Here, we used high-throughput single-nucleus RNA-sequencing to map the cellular and functional heterogeneity of SGCs in human dorsal root ganglion (DRG), and astrocytes, microglia, and oligodendrocytes in human spinal cord. In addition, we compared the human findings with previous single-nucleus transcriptomic profiles of glial cells from mouse DRG and spinal cord. This work will comprehensively profile glial cells heterogeneity and will provide a powerful resource for probing the cellular basis of human physiological and pathological conditions related to glial cells.

2022-02-24 | GSE189501 | GEO

Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults [paxgene]

Project description:Here we developed a new approach to sepsis diagnosis that integrates host transcriptional profiling with metagenomic broad-range pathogen detection from cell-free plasma RNA and DNA.

2022-08-03 | GSE189400 | GEO

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