Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clinical application of microbial metagenomics

ABSTRACT: In this study we describe some of the challenges of clinical metagenomics through benchtop sequencing of two distinct sample types, designed to highlight current application and opportunities in this field.

PROVIDER: PRJEB10064 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR976801_1.fastq.gz	Fastqsanger.gz
	ERR976801_2.fastq.gz	Fastqsanger.gz
	ERR976802_1.fastq.gz	Fastqsanger.gz
	ERR976802_2.fastq.gz	Fastqsanger.gz
	ERR976828_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

P application

Project description:P application Raw sequence reads

| PRJNA932121 | ENA

N application

Project description:N application Raw sequence reads

| PRJNA552400 | ENA

Adsorptive microtiter plates as solid supports in affinity purification workflows

Project description:Affinity ligands such as antibodies are widely used in (bio)medical research for purifying proteins from complex biological samples. These ligands are generally immobilized onto solid supports which facilitate the separation of captured protein from sample matrix. Adsorptive microtiter plates are commonly used as solid supports prior to immunochemical detection (e.g. immunoassays) but hardly ever prior to LC-MS-based detection, and here we describe some applications, opportunities, and challenges of corresponding workflows.

2021-11-25 | PXD027530 | Pride

Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS

2015-11-01 | GSE74126 | GEO

testosterone application induced H3K27 deacetylation

Project description:testosterone application induced H3K27 deacetylation

| PRJNA1137417 | ENA

Soil with biochar application

Project description:Soil with biochar application Raw sequence reads

| PRJNA938810 | ENA

Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS

Project description:We describe XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only four days and sequencing possible within four hours. Small sizes of the XmaI-RRBS libraries allow their multiplexing and sequencing on the benchtop high-throughput machines. Described here is the first RRBS protocol validated for the Ion Torrent Personal Genome Machine. DNA from MCF7 cell line and 6 normal breast samples (total 7 samples) were subjected to reduced representation bisulfite sequencing analysis (XmaI-RRBS) by using Ion Torrent platform.

2015-11-01 | E-GEOD-74126 | biostudies-arrayexpress

Harnessing Bronchoalveolar Lavage Metagenomics for Distinguishing Lung Cancer from Pulmonary Infectious Diseases

Project description:Recent progress in unbiased metagenomic next-generation sequencing (mNGS) allows simultaneous examination of microbial and host genetic material in a single test. Leveraging affordable bronchoalveolar lavage fluid (BALF) mNGS data, we employed machine learning to create a diagnostic approach distinguishing lung cancer from pulmonary infections, conditions prone to misdiagnosis in clinical settings. This prospective study analyzed BALF-mNGS data from lung cancer and pulmonary infection patients, delineating differences in DNA/RNA microbial composition, bacteriophage abundances, and host responses, including gene expression, transposable element levels, immune cell composition, and tumor fraction derived from copy number variation (CNV). Integrating these metrics into a host/microbe metagenomics-driven machine learning model (Model VI) demonstrated robustness, achieving an AUC of 0.87 (95% CI = 0.857-0.883), sensitivity = 73.8%, and specificity = 84.5% in the training cohort, and an AUC of 0.831 (95% CI = 0.819-0.843), sensitivity = 67.1%, and specificity = 94.4% in the validation cohort for distinguishing lung cancer from pulmonary infections. The application of a rule-in and rule-out strategy-based composite predictive model significantly enhances accuracy (ACC) in distinguishing between lung cancer and tuberculosis (ACC=0.913), fungal infection (ACC=0.955), and bacterial infection (ACC=0.836). These findings highlight the potential of cost-effective mNGS-based analysis as a valuable tool for early differentiation between lung cancer and pulmonary infections, offering significant benefits through a single comprehensive testing.

2024-01-08 | GSE252118 | GEO

Application of single-cell genomics

Project description:Comprehensive application of single-cell genomics

| PRJEB12266 | ENA

An application of statistics to comparative metagenomics.

Project description:BackgroundMetagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments.ResultsHere we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified.ConclusionThe methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

| S-EPMC1473205 | 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