GEO DataSets

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

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platforms:

GPL15091 GPL15144

18 Samples

Download data: TXT

(Submitter supplied) The genome wide transcriptome analysis to identify the M.tuberculosis sigma factor Rv3286c (SigF) dependent transcripts as well as Pristimaycin induced transcripts

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by genome tiling array

Platform:

GPL15144

14 Samples

Download data: TXT

(Submitter supplied) The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF)

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15091

4 Samples

Download data: TXT

(Submitter supplied) The alternative sigma factor sigmaB has an important role in the acquisition of stress-resistance in many gram-positive bacteria. In the foodborne pathogen Bacillus cereus sigmaB is activated strongly upon a heat shock and other stress conditions. Here we describe the identification of the set of sigmaB-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. more...

Organism:

Bacillus cereus ATCC 14579

Type:

Expression profiling by array

Platform:

GPL4406

7 Samples

Download data

(Submitter supplied) In previously published work, we identified three Mycobacterium tuberculosis sigma (s) factor genes responding to heat shock (sigB, sigE and sigH ). Two of them (sigB and sigE ) also responded to SDS exposure. As these responses to stress suggested that the s factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL2787

15 Samples

Download data: TXT

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

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL4057

33 Samples

Download data: GPR

(Submitter supplied) Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. In this work, we have identified the SigE regulon during infection of macrophages Our results indicate that SigE regulates the expression of genes involved in the maintenance of Mtb cell envelope integrity and function (i.e., detoxification and secretion). Keywords: strains comparison

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL4057

23 Samples

Download data: GPR

(Submitter supplied) During lung infection Mycobacterium tuberculosis (Mtb) resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes. In this work we have analyzed by DNA microarray technique the global transcription profile of Mtb infecting primary human macrophages in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of Mtb. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL4057

11 Samples

Download data: GPR

(Submitter supplied) Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic aa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain revealed that expression of the SigF regulon is strongly induced in the aa3 mutant relative to the wild-type strain

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28938

6 Samples

Download data: TXT

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

Organism:

Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platforms:

GPL14591 GPL14580

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:

Mycobacterium tuberculosis H37Rv; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platforms:

GPL14591 GPL14580

2 Samples

Download data: GPR

(Submitter supplied) We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18886

1 Sample

Download data: GFF

(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) To identify the FurA regulon in Mycobacterium smegmatis MC2 155, we constructed a furA triple mutant with deletion of three furA paralogous genes (MSMEG_6383, MSMEG_3460, and MSMEG_6253) and profiled the transcriptomes of the wild-type and furA triple mutant strains. Differentially expressed genes were identified pair-wisely by means of the edgeR package in R language. 742 genes were differentially expressed in the furA triple mutant compared to the wild-type strain.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23277

6 Samples

Download data: TXT

(Submitter supplied) Nostoc punctiforme is a filamentous cyanobacterium capable if differentiating normal vegetative cells into nitrogen fixing heterocysts and spore-like akinetes. Here the effects of a sigma factor (sigG) mutation on the transcriptome was analyzed under 1) normal vegetative growth, and 2) following akinete induction. A zwf strain grown with fructose differentiates into akinetes following transfer to darkness. more...

Organism:

Nostoc punctiforme

Type:

Expression profiling by array

Platform:

GPL19195

2 Samples

Download data: TXT

(Submitter supplied) DNA Microarray based comparison of M. tuberculosis and its isogenic delta-sigmaH mutant for an extended period of time, using a diamide-stress and removal strategy (post-diamide stress or PDS) Raw data has been requested of, but not provided by, the submitter.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL8382

12 Samples

Download data

(Submitter supplied) The goal of this study was to compare the transcriptome between wild type strain of Listeria monocytogenes and delete nmlR mutant strain of L. monocytogenes using NGS. Method: Duplicate samples of rRNA depleted RNA from wild type and mutants were used to study transcriptomes by ion torrent platform. Transcriptomes of wild type and nmlR mutant were compared by EDGE-pro program. Result: Differential expression by EDGE-pro showed 74 genes with differential expressions between wild type and nmlR null mutant (46 genes were negatively regluated and 28 genes were positively regulated by NmlR).

Organism:

Listeria monocytogenes 10403S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20617

4 Samples

Download data: TXT