GEO DataSets

(Submitter supplied) To potentially understand how H. ducreyi responds to membrane stress, here we defined RpoE-dependent genes using RNA-Seq. We identified 180 RpoE-dependent genes, of which 98% were upregulated; a major set of these genes encodes homologues of envelope maintenance and repair factors. We also identified and validated a putative RpoE promoter consensus sequence, which was enriched in the majority of RpoE-dependent targets. more...

Organism:

[Haemophilus] ducreyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21166

24 Samples

Download data: XLSX

(Submitter supplied) To better understand the role of H. ducreyi CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. Activation of CpxR by deletion of cpxA repressed nearly 70% of its targets, including seven established virulence determinants. Inactivation of CpxR by deletion of cpxR differentially regulated few genes and increased the expression of one virulence determinant. more...

Organism:

[Haemophilus] ducreyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21166

36 Samples

Download data: XLSX

(Submitter supplied) Haemophilus ducreyi 35000HPcpxRpML125 which over-expresses CpxR in a CpxR deletion background, was compared to it vector alone counterpart (35000HPcpxRpLS88) in hopes to elucidate members of the CpxRA regulon.

Organism:

[Haemophilus] ducreyi 35000HP; [Haemophilus] ducreyi

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) Comparative analysis of the global gene expression of a Haemophilus ducreyi 35000HP cpxA deletion mutant relative to the wild type strain

Organism:

[Haemophilus] ducreyi 35000HP; [Haemophilus] ducreyi

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) To better understand the molecular mechanisms underlying Haemophilus ducreyi infection in humans, here we determined the transcriptional profile of H. ducreyi in human lesions using RNA-Seq and compared it to that of in vitro growth. We were able to show that the in vivo transcriptome did not resemble that of in vitro growth. Compared to the inoculum, H. ducreyi harvested from pustules differentially expressed ~120 genes, of which 68 were upregulated. more...

Organism:

[Haemophilus] ducreyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21166

4 Samples

Download data: XLSX

(Submitter supplied) Haemophilus ducreyi 35000HP was subjected to different in vitro growth conditions that resemble the in vivo host environment (presence of serum), in order to ascertain the overall changes in gene expression. This information might identify genes important for colonization and/or survival inside the host.

Organism:

[Haemophilus] ducreyi 35000HP

Type:

Expression profiling by array

Platform:

GPL7741

4 Samples

Download data: GPR

(Submitter supplied) The goal of this study was to compare the global trascription profile of a Haemophilus ducreyi hfq deletion mutant to that of the wild type parental strain.

Organism:

[Haemophilus] ducreyi 35000HP; [Haemophilus] ducreyi

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) The goal of this study was to compare the global trascription profile of a Haemophilus ducreyi fis deletion mutant to that of the wild type parental strain.

Organism:

[Haemophilus] ducreyi; [Haemophilus] ducreyi 35000HP

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) To better understand the role of the (p)ppGpp-mediated stringent response in control of H. ducreyi virulence determinants, here we defined genes potentially regulated by either (p)ppGpp or DksA by using RNA-seq. We were able to show that loss of either (p)ppGpp or DksA resulted in dysregulation of multiple genes including several known virulence determinants. We also show that loss of (p)ppGpp or DksA resulted in differential expression of putative H. more...

Organism:

[Haemophilus] ducreyi 35000HP

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19931

36 Samples

Download data: XLSX

(Submitter supplied) The transcriptional response of Haemophilus ducreyi to anaerobiosis was determined over the course of 18 h. Cells were collected from aerobic and anaerobic cultures at 4, 8, or 18 hours .

Organism:

[Haemophilus] ducreyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31188

24 Samples

Download data: TXT

(Submitter supplied) A major gap in understanding infectious diseases is the lack of information about molecular interaction networks between pathogens and the human host. Haemophilus ducreyi causes the genital ulcer disease chancroid in adults and is a leading cause of cutaneous ulcers in children in the tropics. We developed a model in which human volunteers are infected on the upper arm with H. ducreyi until they develop pustules. more...

Organism:

[Haemophilus] ducreyi; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL26639 GPL26640

12 Samples

Download data: TXT

(Submitter supplied) Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an ECF sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

18 Samples

Download data

(Submitter supplied) To better understand the role of Neisseria gonorrhoeae CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. We identified approximately 139 genes differentially expressed between cpxA (Cpx system active) and cpxR (Cpx system inactive) mutants. A large number of the differentially expressed genes encode envelope-localized proteins.

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22011

12 Samples

Download data: XLSX

(Submitter supplied) Few studies have investigated host-bacterial interactions at sites of infection in humans using transcriptomics and metabolomics. Haemophilus ducreyi causes cutaneous ulcers in children and the genital ulcer disease chancroid in adults. We developed a human challenge model in which healthy adult volunteers are infected with H. ducreyi on the upper arm until they develop pustules. Here, we characterized host-pathogen interactions in pustules using transcriptomics and metabolomics and examined interactions between the host transcriptome and metabolome using integrated omics. more...

Organism:

Homo sapiens; [Haemophilus] ducreyi

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32713 GPL24676 GPL31188

20 Samples

Download data: TXT

(Submitter supplied) Citrobacter rodentium is a murine pathogen used to model the intestinal infection caused by Enteropathogenic and Enterohemorrhagic Escherichia coli (EPEC and EHEC), two diarrheal pathogens responsible for morbidity and mortality in developing and developed countries, respectively. During infection, these bacteria must sense and adapt to the gut environment of the host. In order to adapt to changing environmental cues and modulate expression of specific genes, bacteria can use two-component signal transduction systems (TCS). more...

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL25012

12 Samples

Download data: TXT

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

Organism:

Medicago truncatula; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL9757

65 Samples

Download data: CEL

(Submitter supplied) We characterized transcriptomes for strains overexpressing each of the Sinorhizobium meliloti ECF sigma factors the via a plasmid-borne, melibiose-inducible promoter plasmid (PmelA; pCAP11: Pinedo et al. 2008 J Bacteriol 190:2947-2956) compared to control strains carrying the empty vector.

Organism:

Sinorhizobium meliloti; Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL9757

45 Samples

Download data: CEL

(Submitter supplied) We characterized transcriptomes of Sinorhizobium meliloti root nodule bacteria with mutations in sigma factor genes.

Organism:

Medicago truncatula; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL9757

20 Samples

Download data: CEL

(Submitter supplied) Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39) grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039) grown micro-oxically

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL3401

21 Samples

Download data: CEL, CHP

(Submitter supplied) Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL7420

14 Samples

Download data: GPR