GEO DataSets

(Submitter supplied) We investigated the role of basal ppGpp levels in Synechococcus elongatus PCC7942 in adaptation to darkness. We performed RNA-seq experiments using the rel- relA+ and the rel- relAE335Q strain at dusk and during exposure to 12 h of darkness. We show that basal ppGpp levels is not sufficient for restoration of appropriate transcriptional shutdown in response to darkness.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

36 Samples

Download data: XLS

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed ChIP-seq experiments using wild type and the rel- strain at dusk, during exposure to 12 h of darkness and at dawn. We show that the RNA polymerase pausing index is globally lower in the rel- strain.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16957

12 Samples

Download data: XLSX

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed RNA-seq experiments using wild type and the rel- strain at dusk and during exposure to 12 h of darkness. We show that ppGpp is required for correct response to darkness.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

36 Samples

Download data: XLS

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using wild type + relA+ and wild type + relAE335Q strains after induction with theophylline starting at subjective dusk. We show that ppGpp induction inhibits global transcription in light.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

6 Samples

Download data: XLS

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

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

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

Platform:

GPL16957

106 Samples

Download data

(Submitter supplied) We investigated the role of the basal levels of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using the rel- + relA+ and rel- + relAE335Q strains and show that basal levels of ppGpp are required for regulation of global transcription in light.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

8 Samples

Download data: XLS

(Submitter supplied) Rel is an enzyme involved in the metabolism of ppGpp. We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light and after exposure to darkness. We performed RNA-seq experiments using the rel- strain and wild type and show that ppGpp is required for regulation of global transcription in light and in darkness.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

8 Samples

Download data: XLS

(Submitter supplied) Transcriptomic profiles of Pseudomonas protegens H78 and its (p)ppGpp0 relA/spoT mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on Illumina 2500.

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22592

6 Samples

Download data: XLS

(Submitter supplied) Transcriptional profiling to define the stringent response regulon and significance of basal (p)ppGpp levels in E. faecalis OG1RF.

Organism:

Enterococcus faecalis; Enterococcus faecalis OG1RF

Type:

Expression profiling by array

Platform:

GPL15039

48 Samples

Download data: MEV

(Submitter supplied) In this report, codY mutant strains were constructed and used to demonstrate the relationship of (p)ppGpp synthesized by RelP and RelQ with the activation of CodY. In addition, because CodY has not been studied in S. mutans, we used microarrays to demonstrate that this protein function as a global regulator of gene expression in S. mutans. Keywords: stress response, gene knockout analysis

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4340

8 Samples

Download data: MEV

(Submitter supplied) Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL4995

136 Samples

Download data: TXT

(Submitter supplied) The experiment was carried out to study the effect of loss of (p)ppGpp or cyclic di-GMP on the gene expression pattern of Mycobacterium smegmatis MC2 155 strains. The cells were cultured in MB7H9 broth containing 0.2% glycerol and 0.05% Tween 80. The transcriptome analysis was performed using GeneSpring GX12 software. Fold changes were calculated with respect to the median expression of wild type replicates. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL20299

6 Samples

Download data: TXT

(Submitter supplied) The stringent stress response, mediated by the signalling molecule guanosine penta(tetra)-phosphate (p)ppGpp, has recently gained more attraction as a potential new therapeutic target. However, interference of a global mediator could lead to unwanted side effects, therefore warrants detailed mechanistic understanding. We used RNA-Seq to investigate the transcriptional landscape of a Pseudomonas aeruginosa ppGpp-deficient strain under non-stressful conditions. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

6 Samples

Download data: TXT

(Submitter supplied) In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, dramatically reduces the transcription rate in the dark (dark repression), and its cellular functions enormously depend on light as an energy source through photosynthetic activity. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression when illuminated or dark-acclimated cells are treated with photosynthesis inhibitors DCMU or DBMIB. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805; Synechococcus elongatus PCC 6301

Type:

Expression profiling by array

Platform:

GPL8012

28 Samples

Download data: CEL