GEO DataSets

(Submitter supplied) Lung disease due to non-tuberculous mycobacteria (NTM) is rising in incidence. While both 2D cell culture and animal models exist for NTM infections, a major knowledge gap is the early responses of human alveolar and innate immune cells to NTM within the human lung microenvironment. Here we describe development of a humanized, 3D, alveolus lung-on-a-chip (ALoC) model of Mycobacterium fortuitum infection that incorporates only primary human cells such as pulmonary vascular endothelial cells in a vascular channel, and type I and II alveolar cells and monocyte-derived macrophages in an alveolar channel along an air-liquid interface. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TAB

(Submitter supplied) Rationale: Nontuberculous mycobacteria (NTM) infection can promote progressive lung function decline and damage, a condition known as NTM Pulmonary Disease (NTM-PD). Mycobacterium abscessus complex (MABSC) is a common cause of infections in people with cystic fibrosis (pwCF). Here, we performed the first single-cell transcriptome characterization of circulating cellular transcripts in pwCF at risk of MABSC infections. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: TSV

(Submitter supplied) The immunologic features of nontuberculous mycobacterial pulmonary disease (NTM-PD) are largely unclear. This study investigated the immunologic features of NTM-PD using digital spatial profiling techniques. Lung tissues obtained from six patients with NTM-PD between January 1, 2006, and December 31, 2020, at Seoul National University Hospital were subjected to RNA sequencing. Cores from the peribronchial and fibrotic stromal areas were stained with CD3, CD68, and DNASyto13, and gene expression at the whole-transcriptome level was quantified using PCR amplification and Illumina sequencing. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

96 Samples

Download data: DCC, PKC

(Submitter supplied) Appendiceal neoplasms include a heterogeneous group of epithelial and non-epithelial tumors with varying malignant potential. Despite the rise in incidence of appendiceal neoplasms in recent years, limited progress has been made in the understanding, management and therapeutic treatment. To comprehensively characterize the cell types and molecular mechanisms driving cellular remodeling in epithelial appendiceal neoplasms, we performed an integrated scRNA-seq study. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found substantial differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: XLSX

(Submitter supplied) Non-tuberculous mycobacteria (NTM) are emerging pathogens with high intrinsic drug resistance. Among rapidly growing NTM species, Mycobacterium abscessus is among the most pathogenic. Standard of care therapy has led to unacceptable outcomes and demonstrates the urgent need to develop effective, broad-spectrum antimycobacterial regimens. Through synthetic modification of spectinomycin (SPC), an aminocyclitol antibiotic, we have identified a distinct structural subclass of ethylene linked aminomethyl spectinomycins (eAmSPC) that are up to 64-fold more potent against M. more...

Organism:

Mycobacteroides abscessus ATCC 19977

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32999 GPL30122

18 Samples

Download data: TXT

(Submitter supplied) Background: Patients with cystic fibrosis (CF) have an elevated lifetime risk of infection and disease caused by nontuberculous mycobacteria (NTM). Currently, there is no method to predict whether patients with cystic fibrosis will develop disease related to non-tuberculous mycobacteria. In non cystic fibrosis populations, several genetic susceptibility factors have been described. In this study, we examined whether patients with cystic fibrosis demonstrate a similar pattern of genetic susceptibility and explored host immune-related biomarkers predictive of NTM pulmonary disease (NTM-PD). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

42 Samples

Download data: CSV

(Submitter supplied) To understand nontuberculous mycobacterial (NTM) pathogenesis, we evaluated immune responses to Mycobacterium avium (Mav) in asymptomatic individuals with a previous history of M. avium complex lung disease (MACDZ). We analyzed global gene expression in paired Mav-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

67 Samples

Download data: CSV

(Submitter supplied) Bacille Calmette Guerin (BCG) is the only licensed vaccine against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) disease. However, BCG has limited efficacy, necessitating the development of better vaccines. Non-tuberculous mycobacteria (NTM), a distinct lineage from Mtb, are opportunistic pathogens present in the environment. TB endemic countries experience higher exposure to NTM, but previous studies have not elucidated the relationship between NTM exposure and BCG efficacy. more...

Organism:

Mus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23642

8 Samples

Download data: MTX, TSV

(Submitter supplied) Immunological mechanisms of susceptibility to NTM disease are poorly understood. We evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex in individuals with MAC lung disease. We investigated the gene expression changes induced in PBMCs by polyclonal stimulation (anti-CD3, anti-CD28), Mav and Mtb lysates and a peptide pool (MTB300) in individuals with MAC lung disease (MACDZ), and healthy controls (IGRA+ and IGRA-).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

198 Samples

Download data: TSV

(Submitter supplied) Mycobacterium abscessus is one of the common clinical non-tuberculous mycobacteria (NTM) which can cause severe skin infections. 5-Aminolevulinic acid photodynamic therapy (ALA_PDT) is an emerming effective antimicrobial medication. To explore whether ALA_PDT can treat M. abscessus infections, we found that ALA_PDT can kill M. abscesses via colony forming unit method. ALA_PDT promoted ferroptosis-like death of M. more...

Organism:

Mycobacteroides abscessus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31177

9 Samples

Download data: TXT

(Submitter supplied) Multiple Sclerosis (MS) is known to be caused by a genetic predisposition triggered by environmental factors. Despite the knowledge of genetic factors and environmental agents involved, it is largely unclear how they interact. Epigenetics, particularly DNA methylation, represents a model for environmental factors to influence the genome. In this paper, we studied 26 affected and 26 unaffected relatives from 8 MS multiplex families (≥ 3 affected relatives) as part of a multicentric Italian cohort study using Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) run on an Illumina® HiSeq 2500 (2x100 bp). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

102 Samples

Download data: BED, XLS

(Submitter supplied) An opportunistic intracellular pathogen Mycobacterium intracellulare, a member of the nontuberculous mycobacteria (NTM) cluster, causes respiratory disease in immunosuppressed hosts, including companion dogs. The purpose of this study is to investigate a host-M.intracellulare interactome in canine monocyte-derived macrophages during the infection.

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21400

16 Samples

Download data: TXT

(Submitter supplied) Root transcriptomic profile was comparatively studied in a serpentine (TM) and a non-metallicolous (NTM) population of Noccaea goesingensis in order to investigate possible features of Ni hyperaccumulation. The exposure to Ni altered the expression of 403 and 534 probe sets in roots of NTM and TM ecotypes respectively. Only 19 genes were commonly regulated in roots of both ecotypes.

Organism:

Noccaea goesingensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28923

12 Samples

Download data: TXT

(Submitter supplied) An opportunistic intracellular pathogen Mycobacterium avium subsp. hominissuis, a member of the nontuberculous mycobacteria (NTM) cluster, causes respiratory disease in immunosuppressed hosts. In particular, infected companion dogs are a potential role to transmit the agent to children or immunosuppressed people. The purpose of this study is to investigate a host-M. avium hominissuis interactome in canine PBMCs during the infection.

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21400

16 Samples

Download data: TXT

(Submitter supplied) The factors predisposing towards the development of pulmonary non-tuberculous mycobacterial disease (pNTM) and influencing disease progression remain unclear. Impaired immune responses have been reported in individuals with pNTM but data are limited and inconsistent. This study aimed to use gene expression profiling to examine the host response to pNTM. Microarray analysis of whole blood gene expression was performed on 25 subjects with pNTM and 27 uninfected controls with respiratory disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

89 Samples

Download data: CEL

(Submitter supplied) The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 Samples

Download data: CSV, TXT

(Submitter supplied) The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

9 Samples

Download data: TXT

(Submitter supplied) The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

9 Samples

Download data: CSV, IDAT

(Submitter supplied) We sought to elucidate the differentially expressed host factors in bronchoalveolar lavage cells (BALc) from nontuberculous mycobacteria (NTM)-infected subjects by studying the host transcriptome in during infection. A heatmap was created from the normalized expression of selected genes that showed statistically significant differential expression between NTM-infected and uninfected subjects. Genes with similar expression patterns were grouped and the most highly expressed genes are shown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24014

6 Samples

Download data: TXT