GEO DataSets

(Submitter supplied) In order to identify possible RNAs regulated by small RNA NsiR3 we have analyzed the responses to nitrogen removal in a mutant lacking nsiR3 (ΔnsiR3). RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 8 h of nitrogen deprivation.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

4 Samples

Download data: TXT

(Submitter supplied) In order to analyze the responses of a heterocystous cyanobacterium to combined-nitrogen depletion/addition, we have used customized microarrays to identify genes potentially involved in heterocysts differentiation by comparing the responses in the control strain and a hetR mutant unable to differentiate heterocysts. RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 6, 8, 12 or 24 h of nitrogen deprivation. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

20 Samples

Download data: TXT

(Submitter supplied) The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. NtcA-activated canonical promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. more...

Organism:

Anabaena

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17858

2 Samples

Download data: BED, TXT

(Submitter supplied) Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Most frequently, antisense transcription is due to the overlap of mRNAs with long 5’ regions or 3’ ends that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO2-fixing cells and the nitrogen-fixing heterocysts. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29232

6 Samples

Download data: GFF, TXT

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

Organism:

Synechocystis sp. PCC 6803

Type:

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

Platforms:

GPL23245 GPL23246

8 Samples

Download data: BW, TXT

(Submitter supplied) Cyanobacteria are oxygenic photoautotrophs responsible for a substantial proportion of nitrogen fixation and primary production in the hydrosphere. Non-nitrogen fixing cyanobacteria, such as Synechocystis sp. PCC 6803, depend of the availability of nitrogenized species to survive. Therefore, an intricate regulatory network around the transcriptional factor NtcA maintains the homeostasis of nitrogen in these organisms. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23246

4 Samples

Download data: TXT

(Submitter supplied) Cyanobacteria are oxygenic photoautotrophs responsible for a substantial proportion of nitrogen fixation and primary production in the hydrosphere. Non-nitrogen fixing cyanobacteria, such as Synechocystis sp. PCC 6803, depend of the availability of nitrogenized species to survive. Therefore, an intricate regulatory network around the transcriptional factor NtcA maintains the homeostasis of nitrogen in these organisms. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23245

4 Samples

Download data: BW

(Submitter supplied) MicF is a textbook example of a small regulatory RNA (sRNA) that acts on a trans-encoded target mRNA through imperfect base paring. The discovery of MicF as a post-transcriptional repressor of the major Escherichia coli porin OmpF established the paradigm for a meanwhile common mechanism of translational inhibition, through antisense sequestration of a ribosome binding site. However, whether MicF regulates additional genes has remained unknown for almost three decades. more...

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL5780

6 Samples

Download data: TXT

(Submitter supplied) Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self enhancing activator, HetR, and a diffusible inhibitor PatS-5 (RGSGR). more...

Organism:

Nostoc punctiforme PCC 73102

Type:

Expression profiling by array

Platform:

GPL15966

48 Samples

Download data: XYS

(Submitter supplied) Increasing numbers of small, regulatory RNAs (sRNAs) corresponding to 3´ untranslated regions (UTR) are being discovered in bacteria. One such sRNA, denoted GlnZ, corresponds to the 3´ UTR of the Escherichia coli glnA mRNA encoding glutamine synthetase. Several forms of GlnZ, processed from the glnA mRNA, are detected in cells growing with limiting ammonium. GlnZ levels are regulated transcriptionally by the NtrC transcription factor and post-transcriptionally by RNase III. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24570

6 Samples

Download data: TXT

(Submitter supplied) Comparison of gene expression of WT Synechocystis cells with cells overexpressing the sRNA PsrR1 in order to detect direct targets of the sRNA PsrR1.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

10 Samples

Download data: TXT

(Submitter supplied) Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). more...

Organism:

Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28094

24 Samples

Download data: WIG, XLSX