GEO DataSets

(Submitter supplied) DNA methylation affects gene expression in many organisms. To determine to effects of DNA methylation on gene expression in M. tuberculosis, we genetically deleted a predicted DNA methyltransferase encoded by Rv3263 and subjected wildtype, mutant, and complemented strains to global expression analysis.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL17082

9 Samples

Download data: CEL

(Submitter supplied) We determine gene expression profile for the knockout of Rv3263 (DNA Methyltransferase) and compared to wildtype M. tuberculosis.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17967

2 Samples

Download data: TXT, WIG

(Submitter supplied) Transcriptional profile comparison among Beijing and non-Beijing M. tuberculosis isolates.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL8893

6 Samples

Download data: TXT

(Submitter supplied) We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains. Keywords: Basal gene expression comparison

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS1399

Platform:

GPL73

12 Samples

Download data: CEL

Analysis of mutants lacking DNA adenine methyltransferase Dam, or mismatch repair protein MutS, or both. Results help elucidate the global changes resulting from Dam deficiency and the role of mismatch repair in producing these changes.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, transformed count, 4 genotype/variation sets

Platform:

GPL73

Series:

GSE2928

12 Samples

Download data: CEL

(Submitter supplied) Purpose: CsoR, a copper responsive negative regulator of Mycobacterium tuberculosis has been shown to respond to copper and bind to its own regulon in in vitro experiments. Here we examine the role of CsoR in vivo by examining the impact of deletion of csoR on the host transcriptome. Methods: csoR was knocked out of M. tuberculosis H37Rv using the specialized transduction method developed by Bardarov et al (2002), followed by removal of the hygromycin marker with plasmid pYUB870. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18768

4 Samples

Download data: TXT

(Submitter supplied) We previously showed that increased expression of the principal sigma factor, SigA, mediates the capacity of Mycobacterium tuberculosis 210 strains to grow more rapidly in human monocytes, compared to other strains. To identify SigA-regulated genes that favor intracellular mycobacterial growth, we used microarray analysis to compare gene expression between a recombinant M. tuberculosis 210 strain bearing a sense sigA construct and a vector control during growth in MonoMac6 cells. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL4057

4 Samples

Download data: GPR

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

Organism:

Bacillus subtilis; Bacillus subtilis PY79

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL26622 GPL26620

5 Samples

Download data: CSV

(Submitter supplied) We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

Organism:

Bacillus subtilis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26622

1 Sample

Download data: CSV

(Submitter supplied) We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

Organism:

Bacillus subtilis PY79

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26620

4 Samples

Download data: CSV

(Submitter supplied) Since VirS was shown to be upregulated in acidic conditions and MtbΔvirS displayed defect in growth at pH4.5, we performed microarray at pH 6.6 and pH 4.5 to study the role of VirS in regulating gene expression at acidic pH.

Organism:

Mycobacterium tuberculosis str. Erdman = ATCC 35801; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL21002

16 Samples

Download data: TXT, XLSX

(Submitter supplied) The numerous sigma factors present in Mycobacterium tuberculosis (MTB) are indicative of adaptability to different environmental conditions. In this report we describe the sigma factor B (sigB) regulon and the phenotypes of a MTB sigB mutant strain exposed to different stresses like SDS and Diamide. This experiment set compares expression profiles between H37Rv wild type and H37Rv sigB null mutant as well as under different stress conditions. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL8523

36 Samples

Download data

(Submitter supplied) We report RNAseq analysis of Mycobacterium tuberculosis strain that lack transcription factor EmbR and the isogenic wild type. We identify the genes whose expression is altred by the mutation and show that genes associated with virulende are downregulated in EmbR KO cells.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27507

8 Samples

Download data: TXT

(Submitter supplied) Moraxella catarrhalis contains an N6-adenine DNA-methyltransferase (ModM3), that is subject to phase variable expression (random ON/OFF switching). Phase-variable switching of DNA methyltransferase activity results in the presence or absence of methylation at a specific target sequence, leading to co-ordinated, epigenetically-regulated switching of expression of multiple genes across the genome. The suite of genes thus regulated are known as a phasevarion (phase-variable regulon). more...

Organism:

Moraxella catarrhalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27756

6 Samples

Download data: TXT

(Submitter supplied) Unlike many pathogens that are overtly harmful to their hosts, Mycobacterium tuberculosis can persist for years within humans in a clinically latent state. Latency is often linked to hypoxic conditions within the host. Among M. tuberculosis genes induced by hypoxia is a putative transcription factor, Rv3133c/DosR. We performed targeted disruption of this locus followed by transcriptome analysis of wild-type and mutant bacilli. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL5714

12 Samples

Download data: TXT

(Submitter supplied) The Mycobacterium tuberculosis genome encodes two complete high-affinity Pst phosphate-specific transporters. We previously demonstrated that a membrane-spanning component of one Pst system, PstA1, was essential both for M. tuberculosis virulence and for regulation of gene expression in response to external phosphate availability. To determine if the alternative Pst system is similarly required for virulence or gene regulation, we constructed a deletion of pstA2. more...

Organism:

Mycobacterium tuberculosis str. Erdman = ATCC 35801; Mycobacterium tuberculosis CDC1551; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL15398

6 Samples

Download data: GPR

(Submitter supplied) Mycobacterium tuberculosis persists in the lungs of mammalian hosts despite inducing an immune response dominated by the macrophage-activating cytokine interferon-gamma (IFN-gamma). We identified the M. tuberculosis phosphate uptake system component PstA1 as a factor required to resist IFN-gamma dependent immunity. A ∆pstA1 mutant was fully virulent in IFN-gamma-/- mice but was attenuated in mice lacking the IFN-gamma-inducible nitric oxide synthase (NOS2). more...

Organism:

Mycobacterium tuberculosis CDC1551; Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis str. Erdman = ATCC 35801

Type:

Expression profiling by array

Platform:

GPL15398

11 Samples

Download data: GPR

(Submitter supplied) A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the Histone-like Nucleoid-Structuring protein, is one of these NAPs and protects Escherichia coli from foreign gene expression. Though lacking any sequence similarity with E. coli H-NS, Rv3852 was annotated as the H-NS ortholog in Mycobacterium tuberculosis, as it resembles human histone H1. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17280

4 Samples

Download data: TXT

(Submitter supplied) Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, and it is present in different cell types. dA6m is commonly depleted in gene exons, whilst it remains abundant in introns. Finally, we have identified the putative consensus sequence, where there is preferential methylation. more...

Organism:

Escherichia coli; Xenopus laevis; Mus musculus

Type:

Methylation profiling by high throughput sequencing

4 related Platforms

28 Samples

Download data: BW