GEO DataSets

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

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34550

30 Samples

Download data

(Submitter supplied) Among the multidrug-resistant (MDR) clones of Mycobacterium tuberculosis (Mtb) that were epidemiologically particularly successful, the 100-32 MDR Beijing clone, also called B0/W148 clone, has emerged since the early sixties. These B0/W148 strains belonging to the lineage 2 within the global Mtb phylogeny, are the main contributors to the MDR epidemic in Russia and Eastern Europe, and since the USSR’s fall, have also propagated to Western Europe. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34550

12 Samples

Download data: TXT

(Submitter supplied) Among the multidrug-resistant (MDR) clones of Mycobacterium tuberculosis (Mtb) that were epidemiologically particularly successful, the 100-32 MDR Beijing clone, also called B0/W148 clone, has emerged since the early sixties. These B0/W148 strains belonging to the lineage 2 within the global Mtb phylogeny, are the main contributors to the MDR epidemic in Russia and Eastern Europe, and since the USSR’s fall, have also propagated to Western Europe. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34550

18 Samples

Download data: TXT

(Submitter supplied) The ability ofMycobacterium tuberculosis(Mtb) to tolerate nitric oxide (NO) and superoxide (O2•−) produced by phagocytes contributes to its success as a human pathogen. Recombination of NO and O2•− generates peroxynitrite (ONOO­-­), a potent oxidant produced inside immunologically-activated macrophages and causes lethality in diverse organisms. However, while the response ofMtbtowards NO and O2•− is well established, howMtbresponds to ONOO­- remains uncertain. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20677

6 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis's autarkic lifestyle within the host involves rewiring its transcriptional networks to combat host-induced stresses. With the help of RNA-seq, we identified Mtb pathways that are upregulated in response to oxidative, nitrosative, acidic, starvation, and surfactant stresses. Genes belonging to sulfur metabolism were found to be significantly upregulated during oxidative stress. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29178

28 Samples

Download data: TSV

(Submitter supplied) Tuberculosis (TB) is an ancient disease caused by the intracellular bacterial pathogen Mycobacterium tuberculosis (Mtb). The rise of antimicrobial resistance (AMR) threatens to bring Mtb to the forefront of bacterial pathogens as the current treatments are increasingly becoming ineffective. Understanding the development of AMR and the virulence processes of Mtb is crucial for the identification of new drug targets and the rational design of anti-TB treatments. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL34550

5 Samples

Download data: XLSX

(Submitter supplied) Using Total RNA sequencing, We report the effects of VapC13 and VapC26 overexpression on the transcriptome of M. tuberculosis. For RNA-seq experiments, early-log phase cultures (OD600nm ~ 0.2-0.3) of M. tuberculosis strains harboring either pTetR or pTetR-vapC13 or pTetR-vapC26 were induced with the addition of 50 ng/ml Atc for 24 h. For total RNA isolation, induced cultures were harvested by centrifugation, washed twice with 1x PBS and lysed by bead beating in Trizol. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29178

9 Samples

Download data: TXT

(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:

Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv

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