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

Comparison of gene expression in M. tuberculosis TrxB2-TetON-tetO-WT mutant treated or not with atc

ABSTRACT: M. tuberculosis thioredoxin reductase (TrxB2) is essential for Mtb physiology and pathogenesis. To gain insight into its biological functions, we generated the TrxB2-TetON-tetO mutants, in which TrxB2 is partially depleted in the absence of atc without impairing bacterial viability. We grew TrxB2-TetON-tetO-WT in 7H9 medium with 400 ng/ml atc, until the OD reached 0.5~0.6. Then Mtb was washed with 7H9 medium 3 times and suspended in 7H9 medium with or without atc. Then samples were taken 24, 48, 72 and 120 hrs later.

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Kan Lin

PROVIDER: E-GEOD-72328 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of gene expression in M. tuberculosis TrxB2-DUC mutant treated or not with atc

Project description:M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the mechanisms underlying lethality caused by TrxB2 depletion, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc. We grew bacteria in 7H9 medium to an OD of 0.5~0.6 and then added atc to a final concentration of 400ng/ml. Samples were collected 6 h and 24 h after atc treatment.

2016-05-12 | E-GEOD-72329 | biostudies-arrayexpress

Comparison of gene expression in M. tuberculosis TrxB2-DUC mutant treated or not with atc and DTT

Project description:M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the pathways dependent on TrxB2, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc and DTT. We grew bacteria in 7H9 medium to an OD of 0.5~0.6. We then added atc to a final concentration of 800 ng/ml and DTT to a final concentration of 2 mM. Samples were collected 24 hr after treatment.

2016-05-12 | E-GEOD-78894 | biostudies-arrayexpress

Comparison of gene expression in M. tuberculosis TrxB2-TetON-tetO-WT mutant treated or not with atc

Project description:M. tuberculosis thioredoxin reductase (TrxB2) is essential for Mtb physiology and pathogenesis. To gain insight into its biological functions, we generated the TrxB2-TetON-tetO mutants, in which TrxB2 is partially depleted in the absence of atc without impairing bacterial viability.

2016-05-12 | GSE72328 | GEO

M. tuberculosis (Mtb) Produces Nitrite in Human Macrophages in Physiologic Oxygen to Impact Mycobacterial ATP Consumption and Gene Expression

Project description:We sequenced mRNA from Mtb that had been treated with 5 mM nitrate or was untreated in standard 7H9/ADNaCl medium. This generated the first analysis of gene expression following mycobacterial nitrate respiration. Examination of mRNA levels in Mtb following nitrate respiration, which results in the production of nitrite.

2013-10-21 | E-GEOD-51037 | biostudies-arrayexpress

Comparison of gene expression in M. tuberculosis TrxB2 mutants

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

2016-05-12 | E-GEOD-72330 | biostudies-arrayexpress

Transcriptional changes associated with chemical induction of adenylyl cyclase activity in Mtb

Project description:Goal: Assess transcriptional changes in Mtb associated with activation of adenylyl cyclase activity in the bacterium, by treatment with the Rv1625c agonist V-59 or activation of the TetOn-cAMP construct. Specifically, address changes in transcription of cholestrrol utilization genes, during growth of Mtb in cholesterol media. Method: WT, Rv1625c knockout, and Rv1625c Complement strains of Mtb were grown in cholesterol-based media and treated with V-59 or vehicle control (DMSO). V-59 is known to increase cAMP synthesis in WT, but not in Rv1625c knockout Mtb. V-59 increases cAMP synthesis above that observed in WT in the Complement strain, due to Rv1625c overexpression in this strain. Also, utilized TetOn-cAMP Mtb strain, to induce cAMP synthesis independent of V-59 and Rv1625c. Treatment with Atc induces expression of catalytic domain of Rv1264 in this strain. We grew the TetOn-cAMP strain in cholesterol-based media, treated with Atc or EtOH (vehicle control). Conclusions: Transcriptional changes to cholesterol utilization genes associated with V-59 treatment in WT Mtb were similar to those associated with TetOn-cAMP induction. The transcriptional changes associated with blockade of cholesterol degradation following V-59 treatment in WT Mtb were not observed in the Rv1625c knockout strain. The Rv1625c knockout strain had intrinsic defects in induction of cholesterol utilization genes. The Complement strain showed enhanced transcriptional changes in response to V-59 treatment.

2021-12-16 | GSE190875 | GEO

The carbonic anhydrase inhibitor ethoxzolamide inhibits the Mycobacterium tuberculosis PhoPR regulon and Esx-1 secretion and attenuates virulence

Project description:The purpose of this study was to examine how ethoxzolamide modulates gene M. tuberculosis gene expression at acidic pH. We observed that ethoxzolamide downregulates genes of the PhoPR regulon. Mtb strain CDC1551 was grown at 37C in T-25 vented, standing tissue culture flasks in 8 ml of buffered 7H9 medium seeded an initial OD of 0.2. Three conditions were examined with two biological replicates: 1) DMSO treated, pH 7.0, 2) DMSO treated, pH 5.7, 3) 40 µM ethoxzolamide treated, pH 5.7. The CDC1551(phoP::Tn) mutant was grown in a similar manner and treated with DMSO at pH 7.0 and 5.7. Following six days incubation, total bacterial RNA was extracted and analyzed as previously described.

2015-05-20 | E-GEOD-63917 | biostudies-arrayexpress

Mycobacterium tuberculosis ESX-3 conditional mutant expression

Project description:Transcriptional profile of esx-3 conditional mutant strain (TB79) vs its parental strain (TB38) grown in 7H9 in presence of 100ng/ml Atc for 48h One experimental condition. 2 independent biological replicates. One replicate per array.

2013-06-12 | E-GEOD-47834 | biostudies-arrayexpress

Effect of hypoxia on Mycobacterium tuberculosis-host phagocyte interactions

Project description:Mtb appears to have developed specialized biomolecular infrastructure to survive and persist within granulomas, where it is subjected to a diverse set of stress conditions. One of these stress conditions is hypoxia. We hypothesized that host cell response is radically altered with hypoxia stressed Mtb and designed in-vitro experiments to study this phenomenon. Hypoxia-stressed as well as aerobically grown Mtb were used to infect rhesus macaque bone marrow derived macrophages (Rh-BMDMs) and the host global transcriptional response compared. Using 4 x44 k Agilent arrays specific for rhesus macaque genome, we tested in biological duplicate the effect of aerogically grown Mtb on rhesus macaque BMDMs and compared this to the corresponding effect of the hypoxia-conditioned Mtb on rhesus macaque BMDMs

2013-05-22 | E-GEOD-47163 | biostudies-arrayexpress

Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein

Project description:The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or negatively, including a key ESX-1 component, the espACD operon. EspR is also thought to be an ESX-1 substrate. Using EspR-specific antibodies in ChIP-Seq experiments (chromatin immunoprecipitation followed by ultra-high throughput DNA sequencing) we show that EspR binds to at least 165 loci on the Mtb genome. Included in the EspR regulon are genes encoding not only EspA, but also EspR itself, the ESX-2 and ESX-5 systems, a host of diverse cell wall functions, such as production of the complex lipid PDIM (phenolthiocerol dimycocerosate) and the PE/PPE cell-surface proteins. EspR binding sites are not restricted to promoter regions and can be clustered. This suggests that rather than functioning as a classical regulatory protein EspR acts globally as a nucleoid-associated protein capable of long-range interactions consistent with a recently established structural model. EspR expression was shown to be growth phase-dependent, peaking in the stationary phase. Overexpression in Mtb strain H37Rv revealed that EspR influences target gene expression both positively or negatively leading to growth arrest. At no stage was EspR secreted into the culture filtrate. Thus, rather than serving as a specific activator of a virulence locus, EspR is a novel nucleoid-associated protein, with both architectural and regulatory roles, that impacts cell wall functions and pathogenesis through multiple genes. ChIP-Seq of EspR in Mtb H37Rv at mid-log phase of growth. Two independent experiments were performed. Input DNA (No IP) was used as a control.

2012-04-02 | E-GEOD-35149 | 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