Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell-specific methylation patterns in TB patients and household contacts

ABSTRACT: Monocytes and granulocytes were isolated from blood of TB patients and household contacts. DNA was isolated and methylation profile was measured using Illumina HumanMethylation450. House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.

ORGANISM(S): Homo sapiens

SUBMITTER: January Weiner

PROVIDER: E-GEOD-72338 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cell-specific microRNA expression patterns in TB patients and household contacts

Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and microRNA expression was measured using microarrays. House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.

2015-08-24 | E-GEOD-70425 | biostudies-arrayexpress

Cell-specific gene expression patterns in TB patients and household contacts

Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and gene expression was measured using microarrays. House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.

2015-08-24 | E-GEOD-70476 | biostudies-arrayexpress

Blood Transcriptional Profiling of a prospective HIV-negative UK Cohort of Tuberculosis Contacts

Project description:Blood transcriptional signatures may predate clinical diagnosis and detect subclinical incipient tuberculosis (TB) disease. To validate such blood signatures, close contacts of TB patients were recruited from multiple TB clinics in London. Close contacts of active TB were defined as individuals with a cumulative duration of exposure of greater than eight hours in a confined space to the index case prior to initiation of treatment. Known human immunodeficiency virus (HIV)-positive patients were excluded. At enrolment, interferon gamma release assays (IGRAs) were done using the QuantiFERON-TB Plus assay (Qiagen, Germany), and peripheral blood was collected into Tempus tubes for whole genome transcriptional profiling by RNA sequencing. Participants who progressed to active TB were identified by linkage with the national electronic TB register. Local case notes were reviewed to identify individuals who had received preventative treatment. This submission contains data from n=360 adult participants, of which n=9 progressed to TB during a median follow-up time of 1.9 years. The data were used for two publications: The first publication (Roe et al 2019) makes use of an initial subset of n=333 participants, of which n=6 progressed to TB during the median follow-up time of 346 days. In the second publication (Gupta et al 2019), we extended the dataset to n=360 participants and the median follow-up time to 1.9 years; n=3 initial non-progressors progressed to TB during this extended follow-up.

2019-08-29 | E-MTAB-6845 | biostudies-arrayexpress

Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-22 | E-GEOD-70478 | biostudies-arrayexpress

Tuberculosis diagnostic biomarker signature by proteomics and metabolomics

Project description:: Tuberculosis (TB) is a transmissible disease listed as one of the 10 leading causes of death worldwide (10 million infected in 2019). A swift and precise diagnosis is essential to forestall its transmission, for which is crucial the discovery of effective diagnostic biomarkers. In this study, we aimed to discover molecular biomarkers for the early diagnosis of tuberculosis. Two independent cohorts comprising 29 and 34 subjects were assayed by proteomics, and 49 were included for metabolomic analysis. All subjects were arranged into 3 experimental groups – healthy controls (Controls), Latent TB infection (LTBI) and TB patients. LC-MS/MS blood serum protein and metabolite levels were submitted to univariate, multivariate and ROC analysis. From the 149 proteins quantified in the discovery set, 25 were found to be differentially abundant between Controls and TB patients. The AUC, specificity and sensitivity, determined by ROC statistical analysis of the model composed by four of these proteins considering both proteomic sets, were 0.96; 93% and 91%, respectively. The five metabolites (9-methyluric acid, indole-3-lactic acid, trans-3-indoleacrylic acid, hexanoylglycine and N-acetyl-L-leucine) that better discriminate the control and TB patient groups (VIP > 1.75) from a total of 92 metabolites quantified in both ionization modes, were submitted to ROC analysis. An AUC=1 was determined with all samples being correctly assigned to the respective experimental group. An integrated ROC analysis enrolling 1 protein and 4 metabolites was also performed for the common control and TB patients in the proteomic and metabolomic groups. This combined signature has correctly assigned the 12 controls and 12 patients used only for prediction (AUC=1, specificity=100% and sensitivity=100%). This multi-omics approach has revealed a biomarker signature for tuberculosis diagnosis that could be potentially used for developing a point-of-care diagnosis clinical test.

2023-03-11 | PXD037341 | Pride

Discovery of plasma/serum protein biomarkers for progression from Mycobacterium tuberculosis infection to disease

Project description:The overall scope of this study is to find early tuberculosis (TB) candidate protein biomarkers in different TB study groups vs. controls. The identified biomarkers may become the basis of a rapid diagnostic test able to identify active TB earlier than current practice. In addition, the candidate biomarkers may predict which patients are likely to convert from latent infection to active disease. . This project uses plasma and serum samples collected in a long-standing TB household contact study, the Kawempe Community Health Study, conducted in Kampala, Uganda, a TB endemic area. The study utilizes samples from TB index cases and household contacts that were negative for TB at recruitment. A subset of these contacts developed Mtb infection (i.e., their Tuberculin Skin Test (TST) converted to positive) after 3-6 months, and smaller subset developed active TB after 3 months of follow-up. Control patients were still TST negative at 12 months or 24 months of follow-up. This dataset corresponds to the discovery phase of the study.

2019-11-25 | PXD000582 | Pride

Cell-specific gene expression patterns in TB patients and household contacts

Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and gene expression was measured using microarrays.

2015-08-24 | GSE70476 | GEO

Cell-specific microRNA expression patterns in TB patients and household contacts

Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and microRNA expression was measured using microarrays.

2015-08-24 | GSE70425 | GEO

Cell-specific methylation patterns in TB patients and household contacts

Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. DNA was isolated and methylation profile was measured using Illumina HumanMethylation450.

2015-08-25 | GSE72338 | 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

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