GEO DataSets

(Submitter supplied) In this study, we analyze the role of Lsr2 as a transcription factor in M. smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from that of the obligatory mycobacterial pathogens. In summary, the combined RNA-seq and ChIP-seq data revealed that Lsr2 controls gene expression either directly by binding their promoter regions or indirectly through DNA loop formation.

Organism:

Mycolicibacterium smegmatis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29596

4 Samples

Download data: NARROWPEAK

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

Organism:

Mycobacterium tuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17879

12 Samples

Download data: TXT

(Submitter supplied) mIHF is a possible nucleoid associated protein. Its effect on gene regulation remains unknown. We performed an RNA-seq analysis of the mihF conditional knock-down mutant in Mycobacterium tuberculosis. We show that mihF is essential for in vitro growth and that depeltion of mIHF results in deregulation of a large number of genes. Notably, the most downregulated gene was the espACD operon, which is necessary for secretion of M. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17879

8 Samples

Download data: CSV, TXT

(Submitter supplied) mIHF is a possible nucleoid associated protein, but its DNA binding characteristics are unknown. To address this, we performed a ChIP-seq analysis of mIHF in Mycobacterium tuberculosis.

Organism:

Mycobacterium tuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17879

4 Samples

Download data: TXT

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

Organism:

Mycobacterium tuberculosis H37Rv; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platforms:

GPL14580 GPL14591

2 Samples

Download data: GPR

(Submitter supplied) Transcriptional profile of Mycobacterium tuberculosis in in vitro acid-nitrosative multistress, comparing untreated control cells and bacteria under multi-stress.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL14591

1 Sample

Download data: GPR

(Submitter supplied) Transcriptional profile of Mycobacterium smegmatis in in vitro acid-nitrosative multistress, comparing untreated control cells and bacteria under multi-stress.

Organism:

Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platforms:

GPL14580 GPL14591

2 Samples

Download data: GPR

(Submitter supplied) To survive a dynamic host environment, Mycobacterium tuberculosis must endure a series of challenges from reactive oxygen and nitrogen stress, to drastic shifts in oxygen availability. The mycobacterial Lsr2 protein has been implicated in reactive oxygen defense via direct protection of DNA. To examine the role of Lsr2 in pathogenesis and physiology of M. tuberculosis, we generated a strain deleted for lsr2. more...

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis CDC1551

Type:

Expression profiling by array

Platform:

GPL15398

16 Samples

Download data: GPR

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

Organism:

Mycobacteroides abscessus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL29518 GPL33637

22 Samples

Download data: BW

(Submitter supplied) Mycobacterium abscessus (Mabs) is a fast-growing, non-tuberculous mycobacterium responsible for serious lung infections in patients with cystic fibrosis. This bacterium evolves during the pulmonary infection between a smooth (S) and a rough morphotype (R). We have previously isolated the lsr2 gene as being differentially expressed during the transition between Mabs-S and Mabs-R. lsr2 encodes a pleiotropic transcription factor belonging to the superfamily of nucleoid-associated proteins (NAPs), which play an essential role in the hierarchical organization of bacterial chromosomes. more...

Organism:

Mycobacteroides abscessus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33637

10 Samples

Download data: BW

(Submitter supplied) Mycobacterium abscessus (Mabs) is a fast-growing, non-tuberculous mycobacterium responsible for serious lung infections in patients with cystic fibrosis. This bacterium evolves during the pulmonary infection between a smooth (S) and a rough morphotype (R). We have previously isolated the lsr2 gene as being differentially expressed during the transition between Mabs-S and Mabs-R. lsr2 encodes a pleiotropic transcription factor belonging to the superfamily of nucleoid-associated proteins (NAPs), which play an essential role in the hierarchical organization of bacterial chromosomes. more...

Organism:

Mycobacteroides abscessus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29518

12 Samples

Download data: XLSX

(Submitter supplied) Transcriptional profiling of M. smegmatis and Dcrp1 grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol. Transcriptional profiling of M.smegmatis HLA102 harboring tetracycline inducible vector pMind containing the Crp2 and M. smegmatis harboring pMind grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol

Organism:

Mycolicibacterium smegmatis; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL18444

8 Samples

Download data: TXT

(Submitter supplied) Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis ΔsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL9823

8 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in a Mycobacterium smegmatis mc2 155 delta-MSMEG_0166 mutant, compared to the wild-type strain. MSMEG_0166 is a transcriptional regulator in the gntR family. Mutations in MSMEG_0166 result in hypersensitivity to the bactericidal ubiquitin peptide Ub2, as well as oxidative stress caused by either organic or inorganic agents

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL11392

6 Samples

Download data: PAIR

(Submitter supplied) The study was conducted to understand the role of F6 small non-coding RNA in M.smegmatis. The results are a description of transcriptome changes in M. smegmaits strain with deletion of a gene of small RNA F6 relative to wild type strain.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26210

6 Samples

Download data: CSV, TXT

(Submitter supplied) Comparing transciptional profile of a M. smegmatis mc2155 ΔsigF strain and wild type (control) in in vitro culture at two time points (exponential phase and stationary phase) for identification of SigF-dependent genes.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by array

Platform:

GPL5862

8 Samples

Download data: TXT

(Submitter supplied) DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by array

Platform:

GPL5862

4 Samples

Download data: MEV, TXT

(Submitter supplied) We report the regulatory effect of a novel family of nucleoid-associated protein in Streptomyces coelicolor

Organism:

Streptomyces coelicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29790

12 Samples

Download data: TXT

(Submitter supplied) We report the DNA binding profile of a novel family of nucleoid-associated protein in Streptomyces coelicolor

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29676

4 Samples

Download data: TXT