GEO DataSets

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Iron (Fe) and phosphorus (P) are essential nutrients with close geochemical association. They exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. However, the adaptive strategies of photosynthetic organisms to Fe/P co-limitation remain largely unknown. Here, we show that phosphorus deficiency increases the growth of Fe-limited cyanobacteria through a PhoB-mediated regulatory network. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31267

4 Samples

Download data: BED, TDF, XLS

(Submitter supplied) Thioredoxins play an essential role in regulating enzyme activity upon response to environmental changes, especially in photosynthetic organisms. These are crucial for the regulation of metabolism in cyanobacteria, but the key central processes redox-regulated remain to be determined. Physiological, metabolic and transcriptomic characterization of a conditional mutant of the essential trxA gene in Synechocystis (STXA2) revealed that reduced TrxA levels alter cell morphology and enter in a dormant-like state. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

17 Samples

Download data: TXT

(Submitter supplied) The mechanisms of acclimating to a nitrogen-fluctuating environment are necessary for the survival of aquatic cyanobacteria in their natural habitats, but our understanding is still far from complete. Here, the synthesis of phycobiliprotein is confirmed to be much earlier than that of photosystem components during recovery from nitrogen chlorosis and an unknown protein Ssr1698 is discovered to be involved in this synthetic process. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31267

6 Samples

Download data: TXT

(Submitter supplied) The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. more...

Organism:

Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome; Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome; Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22923

8 Samples

Download data: CSV, GFF

(Submitter supplied) Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL21131

12 Samples

Download data: TXT

(Submitter supplied) Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL21131

12 Samples

Download data: TXT

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

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL21131

36 Samples

Download data: TXT

(Submitter supplied) Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL21131

12 Samples

Download data: TXT

(Submitter supplied) Cyanobacteria, photoautotrophic prokaryotes, contribute significantly to the global photosynthesis and require large amounts of the essential micronutrient iron in order to maintain their Fe-rich photosynthetic apparatus. Here we use the model organism Synechocystis sp. PCC 6803 (later referred to Synechocystis) in both, standard and iron stress conditions, to study transcription and post-transcription regulation in iron deprivation. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL23938

32 Samples

Download data: TXT

(Submitter supplied) We reported the transcriptomics files of cyanobacteria treated by compound 4k, which exhibited a good algicidal activity. The results revealed that the transcription of genes in the photosynthesis pathways, such as thylakoid and PSI pathway, were affected by 4k, which was validated by the qPCR results. Photosynthesis parameters was further measured and showed that photosynthesis were significantly affected by 4k treatments.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31267

9 Samples

Download data: TXT

(Submitter supplied) Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that sigB and sigD genes are both induced in bright light and high temperature stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (SigD is an only functional group 2 σ factor), and ΔsigCDE (SigD is an only functional group 2 σ factor) strains in standard, bright light and high temperature conditions revealed that the SigB and SigD factors regulate different set of genes, and that SigB and SigD regulons are highly dependent on stress conditions. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31128

45 Samples

Download data: TSV

(Submitter supplied) In many habitats, microorganisms are exposed to high or fluctuating salinities and evolved specific acclimation strategies to thrive in those environments. Euryhaline microorganisms can grow in a broad range of salinities, from low ionic strength like freshwater up to twofold seawater salinities. Here, we analyzed the salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 in a multi-omics approach by combining transcriptomic, proteomic and metabolomic analyses. The Overall, the comparison of salt-induced proteome and transcriptome changes revealed a good correleation between the proteome and transcriptome that as most the majority of stably up-regulated proteins also showed elevated mRNA transcript levels. However, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably also involves the action of small regulatory RNAs acting at the post-transcriptional level. In addition to the rapid and stable steady upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Moreover, the coordinated induction of several stress proteins known to be involved in iron and oxidative stress responses as well as of mechano-sensitive channels was observed. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Moreover, the massive accumulation of the compatible solute glucosylglycerol had large impact on the overall carbon and nitrogen metabolism. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the post-transcriptional regulation of gene expression. A key endoribonuclease in many bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria such as E. coli have evolved a tightly functioning feedback regulation of RNase E, which is mediated in cis by the rne 5′-untranslated region (5′UTR); however, the mechanisms involved in the control of RNase E in other bacteria have largely remained unknown. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

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

Organism:

Phaeodactylum tricornutum; Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28944 GPL24784

188 Samples

Download data: TXT

(Submitter supplied) Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the model cyanobacteria species Synechocystis. We impose gradual heat stress by increasing the temperature in a stepwise fashion (1.5 °C h-1) from their optimal growth temperature of 30 °C to a maximum temperature of 46.5 °C over a period of 12h.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

72 Samples

Download data: TXT

(Submitter supplied) We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of a thermo-sensitive and a wild-typic RNase E mutant strain of the cyanobacterium Synechocystis sp. PCC6803 (rne(Ts) and rne(WT)) before and after a heat shock. Analysis of changing 5'-monophosphorylated ends revealed RNase E depedent processing sites on a transcriptome-wide level.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22923

12 Samples

Download data: CSV, GFF