U.S. flag

An official website of the United States government

Format
Items per page
Sort by

Send to:

Choose Destination

Links from GEO DataSets

Items: 18

1.

Integrative analysis of the salt stress response in cyanobacteria

(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
Series
Accession:
GSE174316
ID:
200174316
2.

Absence of KpsM (Slr0977) impairs the secretion of extracellular polymeric substances (EPS) and impacts carbon fluxes in Synechocystis sp. PCC 6803

(Submitter supplied) Purpose: To obtain an overview of the metabolic changes associated to the absence of KpsM in Synechocystis, in particular on carbon-related metabolic pathways Methods: The trancriptomes of Synechocystis wild type and kpsM mutant were analyzed by RNA sequencing, using three biological replicates. Cultures were grown until reaching an OD730nm of 1.5. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina®. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29624
6 Samples
Download data: TXT
Series
Accession:
GSE165073
ID:
200165073
3.

Oscillating profiles of global genes in Synechocystis sp. PCC 6803 in diurnal light/dark cyles.

(Submitter supplied) RNA samples from cells collected at twenty four time points in 48-hours diurnal cycles were analyzed, and they compared between each other for transcriptional profiles of global genes
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL21668
24 Samples
Download data: TXT
Series
Accession:
GSE79714
ID:
200079714
4.

CyAbrB2 contributes to the transcriptional regulation of low CO2 acclimation in Synechocystis sp. PCC 6803

(Submitter supplied) Acclimation to low CO2 conditions in cyanobacteria involves the coordinated regulation of genes mainly encoding components of the carbon concentration mechanism (CCM). Making use of several independent microarray datasets a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR and CmpR, whereas the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL15867
16 Samples
Download data: TXT
Series
Accession:
GSE82120
ID:
200082120
5.

Global transcriptome analyses and intracellular regulatory mechanisms of glycine betaine and mycosporine-2-glycine expression in the halotolerant cyanobacterium Halothece sp. PCC 7418 exposed to abiotic stresses II

(Submitter supplied) Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of sa;t-down shock on Halothece transcriptomes were examined using RNA sequencing.
Organism:
Halothece sp. PCC 7418
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32361
2 Samples
Download data: XLSX
Series
Accession:
GSE207763
ID:
200207763
6.

Global transcriptome analyses and intracellular regulatory mechanisms of glycine betaine and mycosporine-2-glycine expression in the halotolerant cyanobacterium Halothece sp. PCC 7418 exposed to abiotic stresses

(Submitter supplied) Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of five different stimuli on Halothece transcriptomes were examined using RNA sequencing. In response to diverse stresses, there were both common and stress-specific transcriptional responses.
Organism:
Halothece sp. PCC 7418
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32361
7 Samples
Download data: TXT
Series
Accession:
GSE206286
ID:
200206286
7.

Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

(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
Series
Accession:
GSE97291
ID:
200097291
8.

Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 [RNA-Seq]

(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
Series
Accession:
GSE97289
ID:
200097289
9.

Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 [ChIP-Seq]

(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
Series
Accession:
GSE97282
ID:
200097282
10.

Integrated transcriptomic and metabolomic characterization of the low-carbon response using an ndhR mutant of Synechocystis sp. PCC 6803

(Submitter supplied) The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms, and, hence it is tightly controlled. We studied the Ci-dependent transcriptional and metabolic regulation in the Synechocystis sp. PCC 6803 wild type compared to a DndhR mutant that is defective in the main transcriptional repressor for Ci acquisition genes, NdhR (CcmR). more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL15867
13 Samples
Download data: TXT
Series
Accession:
GSE63352
ID:
200063352
11.

Integrated functional analysis of engineered carbon limitation in the CO2/HCO3-uptake deficient ∆ndhD3/ndhD4/cmpA/sbtA mutant of Synechocystis sp. PCC 6803

(Submitter supplied) Functional analysis of engineered carbon limitation in the ∆ndhD3/ndhD4/cmpA/sbtA (= ∆4) Synechocystis mutant reveals a global phenocopy of wild type acclimation to low CO2 and multi-layered Ci-regulation.
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL15867
12 Samples
Download data: TXT
Series
Accession:
GSE68250
ID:
200068250
12.

CO2-neutral isoprene production using the cyanobacterium Synechocystis sp. PCC 6803

(Submitter supplied) Cyanobacteria are phototrophic prokaryotes that can convert inorganic carbon as CO2 into organic carbon compounds at the expense of light energy. In addition, they need only a few inorganic nutrients and can be cultivated in high densities using non-arable land and seawater. This features qualified cyanobacteria as attractive organisms for the production of third generation biofuels as part of the development of future CO2-neutral energy production. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL21131
4 Samples
Download data: TXT
Series
Accession:
GSE74940
ID:
200074940
13.

Global proteomic characterization of photosystem II complexes from Synechocystis 6803

(Submitter supplied) In this study, we undertook a global proteomics analysis of isolated PSII complexes, comparing protein profiles of HT3 (C-terminal hexahistidine tagged CP47 protein) to those of deltaPsbV HT3, deltaPsbP HT3, and deltaPsbQ HT3. The sensitivity of these techniques allowed for identification of not only stoichiometric components of active PSII complexes, but also for the identification of proteins that are transiently associated with PSII throughout its lifecycle, such as assembly, repair, or degradation partners. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Other
Platform:
GPL6115
3 Samples
Download data: TXT, ZIP
Series
Accession:
GSE9577
ID:
200009577
14.

The RNA helicase CrhR as a regulatory factor

(Submitter supplied) DEAD-box RNA-helicases catalyze the correct folding of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083) whose inactivation has severe effects on cellular physiology and morphology, particularly under cold stress. In order to identify potential RNA targets of CrhR, custom microarrays containing sequences corresponding to non-coding small RNAs (UTRs, ncRNAs, asRNAs, iRNAs) and all mRNAs were constructed. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL18796
12 Samples
Download data: TXT
Series
Accession:
GSE58544
ID:
200058544
15.

Rhodobacter sphaeroides salt stress response

(Submitter supplied) Two excessive NaCl concentrations (0.25% and 1.5%) and two periods of treatment (7 min and 45 min) were used as moderate- and high-salt sress conditions at early and later stages of response, respectively. As a baseline, samples from cells grown on a standard SIS medium in the same growing system and same illumination were used. Keywords: time course and dose response
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array
Platform:
GPL162
15 Samples
Download data: CEL
Series
Accession:
GSE8082
ID:
200008082
16.

Inference of pathways, non-coding RNAs and regulatory elements during iron deprivation of Synechocystis based on comprehensive expression profiling

(Submitter supplied) Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond to changes in extracellular conditions, but must also keep the concentration of intracellular iron under strict control, as free ferrous iron (Fe2+) can lead to the generation of reactive oxygen species. Due to its role as redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria, but the molecular details how such high quota is tightly regulated have remained obscure. more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL15867
12 Samples
Download data: TXT
Series
Accession:
GSE39804
ID:
200039804
17.

Expression data of Frankia sp. strain CcI6 under salt stress, osmotic stress, and control conditions (no salt/osmotic stress)

(Submitter supplied) Purpose:to identify the response of Frankia sp.strain CcI6 to salt and osmotic stress. Frankia sp.strain CcI6 was exposed to salt and osmotic stress for seven days. RNAseq analysis was carried out to ge an insight into the response of the bacterium under salt and osmotic stress conditons
Organism:
Frankia sp. CcI6
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23095
6 Samples
Download data: TXT
Series
Accession:
GSE95217
ID:
200095217
18.

Comparison of carboxysomal (ccmM) and photorespiratory (glcD1/D2) mutants of Synechocystis sp. PCC 6803 using metabolic and transcriptomic phenotyping

(Submitter supplied) The general acclimation of cyanobacteria to low carbon (LC) conditions includes coordinated alterations of gene expression and metabolism. To analyze possible signals for LC sensing and compensating reactions, we compared wild-type (WT) cells with two mutants of Synechocystis, the carboxysome-less mutant ccmM and the photorespiratory mutant ΔglcD1/D2. Metabolic phenotyping revealed that the mutant ΔccmM accumulated high 2-phosphoglycolate (2PG) levels while the ΔglcD1/D2 mutant accumulated glycolate, indicating oxygenase activity of RubisCO at high carbon (HC). more...
Organism:
Synechocystis sp. PCC 6803
Type:
Expression profiling by array
Platform:
GPL6546
26 Samples
Download data: TXT
Series
Accession:
GSE31672
ID:
200031672
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

db=gds|term=|query=1|qty=5|blobid=MCID_677e32817eb86f557ffb07cf|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center