GEO DataSets

(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) 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) Mycobacterium tuberculosis (Mtb) secretes pathogenicity factors and immunologically active molecules via membrane vesicles. However, nothing is known about the mechanisms involved in mycobacterial vesicle biogenesis. This study investigates molecular determinants of membrane vesicle production in Mtb by analyzing Mtb cells under conditions of high vesicle production: iron limitation and VirR restriction. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

7 Samples

Download data: TSV

(Submitter supplied) The factors that determine the outcome of clinical tuberculosis lie within both the host and the pathogen, Mycobacterium tuberculosis (Mtb). The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of the host-pathogen interface for mammalian and pathogen genetic determinants of disease outcome. To identify host and pathogen genetic drivers of Mtb infection, we infected 19 genotypes from the BXD panel, bred from Mtb-resistant C57BL/6J (B6) and Mtb-susceptible DBA/2J (D2), with a comprehensive library of transposon mutants (TnSeq). more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Other

Platform:

GPL20677

45 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis is exposed to a variety of stresses during a chronic infection, as the immune system simultaneously produces bactericidal compounds and starves the pathogen for essential nutrients. The intramembrane protease, Rip1, plays an important role in the adaptation to these stresses, at least partially by the cleavage of membrane bound transcriptional regulators. Although Rip1 is known to be critical for surviving copper intoxication and nitric oxide exposure, these stresses do not fully account the regulatory protein’s essentiality during infection. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29823

17 Samples

Download data: TXT

(Submitter supplied) An accessible, simple, reliable, next-gen in-vitro platform to further the screening for Mtb drugs and understand TB host-pathogen interaction.

Organism:

Homo sapiens; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL32776

11 Samples

Download data: TXT

(Submitter supplied) The establishment of Mycobacterium tuberculosis (Mtb) long-term infection in vivo depends on several factors, one of which is bacterial availability of key nutrients such as iron. The relation between Fe deprivation inside the granuloma and the capacity of Mtb to accumulate lipids and persist in the absence of growth is not well understood. In this context, current knowledge of how Mtb modifies its lipid composition in response to iron starvation is scarce.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

8 Samples

Download data: XLSX

(Submitter supplied) We have performred RNA-seq analysis of WT and ∆phoR Mtb H37Rv under normal and acidic stress, to investigate the role of PhoR in maintaning the pH homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. For acid stress, cells at OD600 of 0.6 were pelleted, washed twice with 7H9 medium buffered with 100 mM MOPS or 2N HCl for pH 7.0 or pH 4.5, respectively, re-suspended in media of indicated pH, and finally the cells were grown further for 2 hours at 37°C. more...

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17280 GPL18768

12 Samples

Download data: TXT, XLSX

(Submitter supplied) RNA-Seq results accompanying submission of a manuscript: "The orphan response regulator Rv3143 modulates the activity of the NADH dehydrogenase complex (Nuo) in Mycobacterium tuberculosis via protein-protein interactions" describing the function of the Rv3143 "orphan" response regulator of the two-component signal transduction systems family, which enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26169

6 Samples

Download data: TXT

(Submitter supplied) M. tuberculosis H37Rv was grown in vitro in five different conditions, including four stress conditions that could mimic what M. tuberculosis may experience in macrophages. The gene expression profiling was studied. Methods: Mycobacterium tuberculosis H37Rv strain was grown under 5 different conditions, in duplicate. RNAseq was performed. The gene expression was compared and Differential Expression was analyzed. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29178

10 Samples

Download data: TXT

(Submitter supplied) We used three M. tuberculosis strains (WT H37Rv, an RV2752c deletion mutation, and the mutant complemented with an Rv2752c overexpression construct), extracted RNA from log phase cultures, and made RNAseq expression libraries as well as 5'-end-directed libraries.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17280

12 Samples

Download data: TXT, XLSX

(Submitter supplied) In-vivo transcriptome analysis was performed to understand the Mtb adaptation strategies to survive in the host and establish infection in BTB. Gene expression profiling of Mtb within abscesses or necrotic specimens obtained from patients with BTB TB compared to exponentially growing in-vitro Mtb culture using whole genome microarray was studied.

Organism:

Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL25141

8 Samples

Download data: TXT

(Submitter supplied) The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23592

18 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23592 GPL22688

207 Samples

Download data: TXT

(Submitter supplied) Gene expression microarray was performed using early log phase culture at 37 degree and 200 rpm followed by RNA extraction from M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv For gene expression profiling, total RNA was isolated from wild type H37Rv, higB KO mutant strain and complemented strains. The bacterial pellets for M.tb H37Rv wild type, M.tb H37Rv HigB KO mutant strain and complemented strain were resuspended in 1.0 ml TRIzol (Invitrogen Corporation, Carlsbad, CA); mRNA was extracted as per standard protocols and cleaned using RNAeasy columns (Qiagen GmbH, Hilden, Germany). more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL16972

8 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to evaluate the effect of new compounds exposure on gene expression of sensitive and MDR clones of M. tuberculosis

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL4519

18 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptional profiling of Mtb H37Rv infected into THP-1 macrophage cell line and treated with 100 µM vitamin C (vit C) for 96 hours and 144 hours, compared to gene expression profile of untreated bacteria post-infection.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL25141

10 Samples

Download data: TXT, XLSX