Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: mNGS of pulmonary infection in patients with acquired immunodeficiency syndrome

PROVIDER: PRJNA891782 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22024700.fastq.gz	Fastqsanger.gz
	SRR22024701.fastq.gz	Fastqsanger.gz
	SRR22024702.fastq.gz	Fastqsanger.gz
	SRR22024703.fastq.gz	Fastqsanger.gz
	SRR22024704.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 111

Similar Datasets

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

Project description:mNGS for patients with pulmonary infection

| PRJNA1140277 | ENA

Project description:mNGS results from pulmonary infection patients

| PRJNA936669 | ENA

Analysis of gene expression in skin fibroblasts derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)

Project description:Autosomal-dominant hyper-IgE syndrome (AD-HIES, Job’s syndrome) is a primary immunodeficiency caused by loss of function mutations in signal transducer and activator of transcription 3 (STAT3), a critical regulator of diverse cellular processes. In addition to immunological deficits, patients experience severe non-immunological features including skeletal, connective tissue and vascular abnormalities, poor post-infection healing, and subsequent pulmonary failure. The underlying mechanisms of these STAT3-dependent non-immunological features are not understood, preventing the development of targeted treatments. In this study, global gene expression was analysed in the patients skin fibroblasts in order to identify signaling pathway affected by the disease-causing STAT3 mutations with ultimate goal to better understand the disease mechanism and identify promising therapeutic targets.

2020-08-12 | GSE139202 | GEO

Gene expression analysis in endothelial cells derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)

Project description:Autosomal-dominant hyper-IgE syndrome (AD-HIES, Job’s syndrome) is a primary immunodeficiency caused by loss of function mutations in signal transducer and activator of transcription 3 (STAT3), a critical regulator of diverse cellular processes. In addition to immunological deficits, patients experience severe non-immunological features including skeletal, connective tissue and vascular abnormalities, poor post-infection healing, and subsequent pulmonary failure. The underlying mechanisms of these STAT3-dependent non-immunological features are not understood, preventing the development of targeted treatments. In this study, global gene expression was analysed in the patients umbilical vein endothelial cells in order to identify signaling pathway affected by the disease-causing STAT3 mutations with ultimate goal to better understand the disease mechanism and identify promising therapeutic targets.

2020-08-12 | GSE139188 | GEO

Expanded Virome in AIDS

Project description:Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome

| PRJEB9524 | ENA

Pathogenesis and outcome of VA1 astrovirus infection in the human brain are defined by disruption of neural functions and imbalanced host immune responses.

Project description:Infections of the central nervous system (CNS) in humans are on the rise due to changing environmental conditions and increase in vulnerable populations comprised of immunocompromised subjects with primary (genetic) or secondary (acquired) immunodeficiency. Many viruses take the opportunity to invade the CNS by capitalizing on impaired immunity of the host. Here we investigate neuropathogenesis of a rare CNS infection in immunocompromised patients caused by the astrovirus and show that it shares many features with another opportunistic infection of the CNS associated with human immunodeficiency virus. We show that astrovirus infects CNS neurons with a major impact on the brainstem. This leads to disrupted synaptic integrity loss of afferent innervation related to infected neurons and global impairment of both excitatory and inhibitory neurotransmission. In the settings of impaired peripheral adaptive immunity host responses to astrovirus infection are dominated by the microglia-macrophage-phagocytosis axis which may be a common compensatory defense mechanism employed by the CNS against opportunistic infections.

2023-07-18 | GSE201384 | GEO

Blood transcriptional profiling in a prospective observational cohort of South African adults presenting for investigation of possible pulmonary tuberculosis

Project description:Blood transcriptional signatures may discriminate individuals with tuberculosis (TB) from disease-free controls, or from patients with other infectious or respiratory diseases. To systematically evaluate the diagnostic accuracy of published transcriptional signatures in a clinically relevant population with high burden of TB and human immunodeficiency virus (HIV), adults presenting for investigation of possible pulmonary TB were consecutively recruited at a TB clinic in South Africa. At enrolment, peripheral blood was collected in Tempus tubes (for RNA sequencing) and patients provided two sputum samples (for Xpert and liquid culture). Amongst 181 patients (median age 35 years), 44 (24%) were infected with human immunodeficiency virus (HIV). 54 patients (30%) were diagnosed with Xpert- or culture-positive TB. No alternate diagnoses were available for Xpert- and culture-negative non-TB patients.

2020-03-17 | E-MTAB-8290 | biostudies-arrayexpress

null

Project description:Card mNGS infection

| PRJEB72354 | ENA

Proteomic profiling of healthy and SLE isolated B-cells

Project description:B cells orchestrate the autoimmune responses in patients with systemic lupus erythematosus (SLE), but broad based B-cell directed therapies only show modest efficacy while attenuating humoral immune responses to vaccines and inducing acquired immunodeficiency. used proteomic and transcriptomic analyses of B cells from patients with SLE and healthy individuals and demonstrated a dominant DDR in SLE B cells.

2022-08-26 | PXD031389 | Pride

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