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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mycobacterium tuberculosis Growth After Aerobic Expression of the DosR Regulon

ABSTRACT: Investigation of whole genome gene expression of M. tuberculosis strain H37Rv:deltaRv3133c::pEXNF-3133c following ectopic expression of a plasmid-borne copy of wildtype Rv3133c compared the same strain with Rv3133c uninduced. The M. tuberculosis H37Rv:deltaRv3133c was originally described in Mol Microbiol. 2003 May; 48(3): 833–843. A six chip experiment in which total RNA from H37Rv:deltaRv3133c::pEXNF-3133c was collected after 24 hours of treatment with chemical expression inducer or vehicle control. Three separate cultures/biological replicates were interrogated for both induced and uninduced samples. Labeled cDNA was hybridized to NimbleGen spotted oligo tiling arrays covering both strands of the M. tuberculosis genome at ~200 bp intervals between 60-mer probes.

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Kyle Minch

PROVIDER: E-GEOD-33752 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mycobacterium tuberculosis Growth After Aerobic Expression of the DosR Regulon

Project description:Investigation of whole genome gene expression of M. tuberculosis strain H37Rv:deltaRv3133c::pEXNF-3133c following ectopic expression of a plasmid-borne copy of wildtype Rv3133c compared the same strain with Rv3133c uninduced. The M. tuberculosis H37Rv:deltaRv3133c was originally described in Mol Microbiol. 2003 May; 48(3): 833–843.

2012-01-31 | GSE33752 | GEO

Expression Analysis of WR99210-treated Mycobacterium tuberculosis H37Rv

Project description:Investigation of whole genome gene expression level changes in Mycobacterium tuberculosis treated with the DHFR inhibitor WR99210, compared to untreated cells. The antimycobacterial properties of WR99210 are further described in Gerum, A., Ulmer, J., Jacobus, D., Jensen, N., Sherman, D., and C. Sibley. 2002. Novel Saccharomyces cerevisiae screen identifies WR99210 analogues that inhibit Mycobacterium tuberculosis dihydrofolate reductase. Antimicrob Agents Chemother 46(11):3362-3369 [PMID:12384337] A nine chip experiment in which total RNA was collected from H37Rv after treatment with 100 uM WR99210 for 0, 4, and 24 hours. Three separate cultures/biological replicates were interrogated for both treated and untreated cultures. Labeled cDNA was hybridized to NimbleGen spotted oligo tiling arrays covering both strands of the M. tuberculosis genome at ~200 bp intervals between 60-mer probes.

2012-09-18 | E-GEOD-40917 | biostudies-arrayexpress

mRNA degradation in Mycobacterium tuberculosis with DosR ectopically induced

Project description:After induction of DosR from a tet regulated promoter (uninduced controls were treated with an equivalent ammount of the solvent, DMSO), transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0. Three replicates for each condition (DosR induced and uninduced) were sampled after 0, 10, 20, 30, and 60 minutes of mRNA decay for a total of 30 arrays.

2012-03-08 | E-GEOD-36344 | biostudies-arrayexpress

Towards understanding the biological function of the unusual chaperonin GroEL1 of Mycobacterium tuberculosis

Project description:Expression data from wild type (H37Rv) and GroEL1(H37RvΔgroEL1::Hyg) mutant strains under a range of environmental stresses The 60 kDa heat shock proteins, also known as GroELs are components of the essential protein folding machinery of the cell, but are also dominant antigens in many infectious diseases. Although generally essential for cellular survival, in some organisms such as Mycobacterium tuberculosis, one or more paralogous GroELs are known to be dispensable. In M. tuberculosis, groEL2 is essential for cell survival, but the biological role of the non-essential GroEL1 is still elusive. To understand the relevance of GroEL1 in M. tuberculosis physiology, detailed transcriptomic analyses for the wild type H37Rv and groEL1 knockout (groEL1 KO) were performed under in vitro stress conditions: stationary phase, cold shock, low aeration, mild cold shock and low pH. Additionally, the survival of the groEL1 KO was assessed in macrophages at multiplicity of infection (MOI) of 1:1 and 1:5. We observed that survival under low aeration was significantly compromised in the groEL1 KO. Further, the gene expression analyses under low aeration showed change in expression of several key virulence factors like two component system PhoP/R and MprA/B, sigma factors sigG, M and H and adversely affected known hypoxia response regulators Rv0081, Rv0023 and DosR. Our work is therefore suggestive of an important role of GroEL1 for survival under low aeration by affecting the expression of genes known for hypoxia response. Expression data from wild type and GroEL1 mutant strains in response to 8 environmental stresses plus log phase growth, with at least three biological replicates of each.

2015-05-14 | E-GEOD-68856 | biostudies-arrayexpress

Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner [II]

Project description:Transcriptional profiling of bacterial RNA samples from infected Rhesus Bone Marrow Derived Macrophages (RhBMDMs) compared to RNA isolated from respective in vitro grwon cultures viz M. tuberculosis H37Rv or Isogeneic mutant MtbdosS

2018-08-22 | GSE118867 | GEO

Folate Pathway Disruption Leads to Critical Depletion of Methionine Derivatives in Mycobacterium tuberculosis

Project description:In this study, screening efforts identified novel antifolates with potent, targeted activity against whole cell Mycobacterium tuberculosis. Liquid chromatography-mass spectrometry analysis of antifolate-treated cultures revealed unique metabolic disruption, including decreased pools of methionine and S-adenosylmethionine. Transcriptomic analysis highlighted up-regulation genes involved in the biosynthesis and utilization of methionine. Supplementation with amino acids or methionine derivatives was sufficient to rescue cultures from MIC-level antifolate treatment. Instead of the “thymineless death” that characterizes folate pathway inhibition in a wide variety of organisms, these data suggest that M. tuberculosis is vulnerable to a critical disruption of the biosynthesis of methionine-derived compounds. These arrays look at the expression profile triggered by exposure to three different anti-folates (WR99210, dimethyl and diethyl methotrexate) in three biological replicates and in a matched set of untreated samples.

2014-03-19 | E-GEOD-55979 | biostudies-arrayexpress

Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response

Project description:Expression data from hypoxic time course and transcription factor over expression experiments. (Abstract from paper will be appended after publication) Hypoxic time course experiments were done with a minimum of 3 replicates. TFOE are matched to the ChIP-seq experiment done simultaneously. This submission consists of the the gene expression component only.

2013-01-12 | E-GEOD-43466 | biostudies-arrayexpress

Mapping and manipulating the M. tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

Project description:Expression data from transcription factor over expression experiments (Abstract from paper will be appended after publication) TFOE are matched to the ChIP-seq experiment done simultaneously.

2014-07-04 | E-GEOD-59086 | biostudies-arrayexpress

M. tuberculosis H37Rv: mutant expressing foreign peptide SL3 Vs control H37Rv

Project description:Transcriptional profiling of M.tb H37Rv cells comparing control wild type H37Rv with H37Rv cells electroporated with constitutive expression plasmid pVV16 expressing ESAT-6 binding peptide SL3. The expression of SL3 makes H37Rv less virulent during ex vivo and BalB/c mice infections, sequesters ESAT-6 inside M.tb cells and cause severe defects in mycobacterial morphology. Goal was to determine the effects of SL3 expression on global H37Rv gene expression. Two color Experiment,Organism: Mycobacterium Tuberculosis, ilife Discoveries designed Custom Mycobacterium tuberculosis on 8x15k GE Microarray. Two-condition experiment, H37Rv vs. H37Rv/SL3. Biological replicates: 2 biological control H37RV replicates labelled with Cy3, 2 SL3 biological expressing replicates labelled with Cy5.

2014-04-10 | E-GEOD-51085 | biostudies-arrayexpress

Phosphoproteomics of Mycobacterium tuberculosis DosR, DosS, and DosT

Project description:Mass Spectrometry based Phosphoproteomics was carried out on M. tuberculosis wild type strain H37Rv and the isogenic mutant strains MtbΔdosR, MtbΔdosS, and MtbΔdosT that were cultured in aerobic as well as hypoxic conditions. During later the oxygen was gradually deprived in cultures that were kept static.

2019-08-31 | PXD015256 | JPOST Repository

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