GEO DataSets

(Submitter supplied) Mycobacterium avium subsp. paratuberculosis (MAP) carries MAP3773c, a putative metal regulator, on its genome which is absent in other mycobacteria. Homologues of this gene in enterobacteria have roles in global iron regulation and homeostasis. The role of MAP3773c in regulating intracellular iron in MAP is poorly understood. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis, sugar metabolism and N-acetyltransferase enhanced intracellular survival genes were downregulated at 30 minutes post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, arginine and proline metabolism, PPE, PE family and mammalian cell entry (MCE) genes were upregulated at that same time point. more...

Organism:

Mycobacterium avium subsp. paratuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33823

20 Samples

Download data: TXT

(Submitter supplied) To further development of our gene expression approach in different groups of leprosy, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish leprosy reactions and relapse cases from healthy controls. Human biopsy and skin slit were collected from reaction cases, PB cases, MB cases, relapse cases and healthy contacts. more...

Organism:

Mycobacterium leprae

Type:

Expression profiling by array

Platform:

GPL33105

45 Samples

Download data: TXT

(Submitter supplied) Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. more...

Organism:

Mycobacterium intracellulare

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33797

9 Samples

Download data: TXT

(Submitter supplied) Superbugs such as drug-resistant Mycobacterium tuberculosis (DR-M.tb) poses a serious global health threat. Upon infection, M.tb reaches the alveolar space and comes in close contact with soluble components of the human alveolar lining fluid (ALF) for an uncertain period of time prior to and following its encounter with alveolar compartment cells. Homeostatic ALF hydrolases, which main function is maintaining lung health, modify the M.tb cell envelope, driving M.tb-host cell interactions. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22688

32 Samples

Download data: TXT

(Submitter supplied) To find potential regulatory targets of the anti-virulence compound S3 in Mycobacterium tubercuolsis.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27507

4 Samples

Download data: TXT

(Submitter supplied) Background: Mycobacterium avium is an opportunistic pathogen that requires complex multidrug treatment. Macrolides, like clarithromycin, are the cornerstone of treatment, but even macrolide-based treatment regimens have suboptimal outcomes. Combining transcriptomic profiling of macrophages and mycobacteria in an in vitro infection model may increase our understanding of the host-pathogen interaction and the effect of antibiotic treatment. more...

Organism:

Mycobacterium avium subsp. hominissuis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32656

6 Samples

Download data: XLSX

(Submitter supplied) Background: Mycobacterium avium complex (MAC) bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and is comprised of a macrolide, a rifamycin and ethambutol; and in severe cases amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. To elucidate these mechanisms, we studied the transcriptomic response to antibiotics and investigated the contribution of efflux and amikacin modification to susceptibility. more...

Organism:

Mycobacterium avium subsp. hominissuis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32656

36 Samples

Download data: XLSX

(Submitter supplied) The transcriptome in response to vitamin B12 was interrogated in three M. tuberculosis Complex species: M. tuberculosis H37Rv, M. tuberculosis GC1237, and M. bovis AF2122/97. Examination of the core B12 transcriptome resulted in a robust differential regulation of 7 genes in the three species analysed

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis variant bovis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26660 GPL17879

12 Samples

Download data: WIG

(Submitter supplied) Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that inflicts major health and economic costs around the world. Mtb encounters diverse environments during its lifecycle and responds to these changes by reprogramming its transcriptional output. However, the mechanisms and regulation of Mtb transcription remains poorly understood. In this work, we simultaneously determine the 5' and 3' ends of individual RNA molecules in Mtb cells using the SEnd-seq method, which enables us to profile the Mtb transcriptome at high resolution. more...

Organism:

Mycobacterium tuberculosis; Mycolicibacterium smegmatis

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL22688 GPL27507 GPL28556

33 Samples

Download data: WIG

(Submitter supplied) Tuberculosis remains the most pervasive infectious disease and the recent emergence of multiple or even fully drug-resistant strains increases the risk and emphasizes the need for more efficient and better drug treatments. A key feature of mycobacteria pathogenesis, conserved between the human pathogen Mycobacterium tuberculosis and the model pathogen Mycobacterium marinum, is the metabolic switch to lipid catabolism during infection and altered expression of virulence genes in coordination with different stages of infection. more...

Organism:

Mycobacterium marinum

Type:

Other

Platform:

GPL33978

40 Samples

Download data: PDF, XLSX

(Submitter supplied) Analyzing differences in transcriptome profile of Mto3DhbhA in 7H9 and Sauton's media compared to control Mto3.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27507

16 Samples

Download data: CSV

(Submitter supplied) To test the consequence of NarS T380 phosphorylation on downstream signaling, we explored transcriptional changes associated with either phosphorylation state.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22688

7 Samples

Download data: CSV

(Submitter supplied) Iron-sulfur (Fe-S) cluster containing proteins are a subset of proteins with crucial functions in the maintenance of cellular physiology throughout all kingdoms of life. The systems involved in the biogenesis and repair of Fe-S clusters hence plays important role in fine-tuning the availability and functionality of Fe-S proteins. Two of the systems known in bacteria are, Isc and Suf. Compared to the facultative anaerobe, E. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

18 Samples

Download data: CSV, TXT

(Submitter supplied) Mycobacterium tuberculosis is the etiological agent of tuberculosis. Mtb is an efficient pathogen partially due to its ability to adapt to the disparate conditions encountered during the course of infection. NO is one of the potent antimicrobial chemicals produced in hosts to tackle pathogens. Mtb is known to respond swiftly to NO-stress. Since, WhiB1 is [4Fe-4S] cluster containing transcription factor with high sensitivity to NO, we evaluate the role of WhiB1 in regulating the cellular transcriptional profile of Mtb in presence or absence of NO.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

8 Samples

Download data: CSV, TXT

(Submitter supplied) RNA-Seq results accompanying submission of a manuscript: "Depletion of CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs" describing the function of the Rv3907c gene product as a CCA-adding enzyme in Mycobacterium tuberculosis.

Organism:

Mycobacterium tuberculosis H37Rv; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL32938 GPL26169

24 Samples

Download data: TXT

(Submitter supplied) We sought to determine the transcriptomic impacts of artemisinin, Artemisia annua extract, and Artemisia afra extract on M. tuberculosis. Log phase cultures were treated with lethal doses for four hours or with inhibitory or sub-inhibitory doses for 24 hours. RNA was collected from untreated controls at the same timepoint.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25317

44 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20677

8 Samples

Download data: BW, TXT

(Submitter supplied) We identified rv0158 gene as a major determinant of redox homeostasis in Mtb. Disruption of rv0158 perturbed redox balance in a carbon source-specific manner, promoted killing in response to anti-TB drugs, reduced survival in macrophages, and persistence in mice. RNA sequencing analysis was performed to identify its regulon. The data indicated that rv0158 is required to balance the deployment of fatty acid substrates between lipid anabolism and oxidation.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

12 Samples

Download data: TXT

(Submitter supplied) The purpose of this study was to determine (i) the interplay between Mycobacterium tuberculosis response to acidic pH and cholesterol, two signals experienced concurrently by the bacterium during host colonization, and (ii) the role of the transcription factor Mce3R in regulation of this response.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17879

16 Samples

Download data: CSV

(Submitter supplied) Vitamin B12 (B12) is an important cofactor in mycobacterial metabolism, and some pathogenic mycobacteria need to obtain it from the host. In this study, we investigated the transport of vitamin B12 in Mycobacterium marinum. We identified a transcriptor regulator that could be potentially involved in the uptake process. RNA sequencing analysis were performed in order to elucidate the regulon of this new transcriptor.

Organism:

Mycobacterium marinum M

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33662

6 Samples

Download data: XLSX