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Items: 1 to 20 of 3881

1.

Half-life estimation in the cyanobacterium Synechocystis sp. PCC 6803 Transcriptome wide during iron starvation

(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
Series
Accession:
GSE209879
ID:
200209879
2.

Transcriptomic response of Nostoc sp. MG11 under desiccation stress

(Submitter supplied) To identify the mechanisms of the adaptation to terrestrial ecosystems, an RNA-seq based transcriptome analysis was conducted on a desiccation resistant cyanobacterium, Nostoc sp. MG11.
Organism:
Nostoc sp. MG11
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32463
2 Samples
Download data: TXT
Series
Accession:
GSE207827
ID:
200207827
3.

Global transcriptional and circadian regulation in a halotolerant cyanobacterium Halothece sp. PCC7418

(Submitter supplied) Substantial evidence has been accumulated about the molecular basis underlying halotolerance; however, insights into the regulatory networks for relevant genes and mechanisms of their interplay remain elusive. Here, we present a comprehensive transcriptome investigation, using RNA sequencing, of specific metabolic pathways and networks in a halotolerant cyanobacterium, Halothece sp. PCC7418, including the circadian rhythm profile. more...
Organism:
Halothece sp. PCC 7418
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32328
24 Samples
Download data: TXT
Series
Accession:
GSE205640
ID:
200205640
4.

Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942

(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; Other
Platform:
GPL32315
46 Samples
Download data: TXT
Series
Accession:
GSE205445
ID:
200205445
5.

Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 [RNA-seq]

(Submitter supplied) Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). more...
Organism:
Synechococcus elongatus PCC 7942 = FACHB-805
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32315
21 Samples
Download data: TXT
Series
Accession:
GSE205444
ID:
200205444
6.

Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 [RB-TnSeq]

(Submitter supplied) Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). more...
Organism:
Synechococcus elongatus PCC 7942 = FACHB-805
Type:
Other
Platform:
GPL32315
25 Samples
Download data: TXT
Series
Accession:
GSE205443
ID:
200205443
7.

RNA-Seq analysis of Synechocystis sp. PCC 6803 with a deletion of the kaiABC gene cluster in comparison to the wild type.

(Submitter supplied) We analyzed the gene expression changes in the wild type and the delta kaiAB1C1 mutant at six time points after a 12 hours dark incubation. RNA-Seq provides a much higher senisitivity and resolution in comparison to previously performed micro array experiments. We aim to get a better understanding how the circadian oscillator which is encoded by the kaiABC genes regulates the overall gene expression in Synechocystis sp. more...
Organism:
Cyanobacterium
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26744
24 Samples
Download data: CSV
Series
Accession:
GSE132275
ID:
200132275
8.

Research on the mode of action of a novel 2-cyclopropyl-4-aminopyrimidine hydrazine compound (4k) for control of cyanobacteria

(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
Series
Accession:
GSE194275
ID:
200194275
9.

Deletion and Complementation of Alr3614 in Anabaena PCC7120

(Submitter supplied) To examine Alr3614 influence on the expression of Anabaena sp. PCC 7120, we have used customized microarrays to identify genes potentially regulated by this short DNA-binding protein. We compared the expression of an Alr3614-deletion strain with an Alr3614-complementation strain.
Organism:
Nostoc sp. PCC 7120 = FACHB-418
Type:
Expression profiling by array
Platform:
GPL25601
4 Samples
Download data: TXT
Series
Accession:
GSE183629
ID:
200183629
10.

Acclimation and stress response of Prochlorococcus to low salinity

(Submitter supplied) Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. more...
Organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. NATL1A
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL31902 GPL31900
12 Samples
Download data: TXT
Series
Accession:
GSE195946
ID:
200195946
11.

Roles of close homologues SigB and SigD in heat and bright light acclimation of the cyanobacterium Synechocystis sp. PCC 6803

(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
Series
Accession:
GSE192357
ID:
200192357
12.

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
13.

Feedback regulation of RNase E during UV-stress response in cyanobacteria

(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
Series
Accession:
GSE186330
ID:
200186330
14.

Thermal transcriptome

(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
Series
Accession:
GSE186039
ID:
200186039
15.

Thermal transcriptome of Synechocystis in response to gradual heat stress

(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
Series
Accession:
GSE186038
ID:
200186038
16.

Genetic responses of metabolically active Limnospira sp. PCC 8005 exposed for one lifecycle to high-dose gamma radiation

(Submitter supplied) Two morphotypes of Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy.h-1 for one mass doubling period under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNAseq transcriptional analysis at approximate time in-tervals of 15, 40, and 71.5 hrs corresponding to cumulative doses of ca. more...
Organism:
Limnospira indica PCC 8005
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30217
12 Samples
Download data: TSV
Series
Accession:
GSE175921
ID:
200175921
17.

Cappable-Seq analysis of the N. punctiforme primary transcriptome during hormogonium development in wild type, and three sigma-factor deletion strains

(Submitter supplied) Cappable-Seq (Ettwiller et. al., BMC Genomics volume 17, Article number: 199 (2016)) was employed to identify transcriptional start sites (TSSs) representing the primary transcriptome of hormogonia, motile filaments of the filamentous cyanobacterium in N. punctiforme ATCC29133. TSSs were defined using the wild-type strain and subsequently the expression of these TSSs was analyzed in each of three sigma-factor deletion mutant strains.
Organism:
Nostoc punctiforme PCC 73102
Type:
Other
Platform:
GPL30445
4 Samples
Download data: WIG, XLSX
Series
Accession:
GSE180983
ID:
200180983
18.

Analysis of transcriptomic changes with a special focus on processing sites in Synechocystis sp. PCC 6803 thermo-sensitive RNase E mutants before and after a 1 h heat shock

(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
Series
Accession:
GSE180316
ID:
200180316
19.

Role of a cryptic tRNA gene operon in the recovery from translation stress

(Submitter supplied) As compared to Eukaryotes, Bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs, which are thought to act in concert for the maintenance of gene translation. Here we show that in some bacteria the tRNA gene set may be partitioned in a housekeeping sub-set that sustains translation, and an inducible one that is generally silent but can be largely induced to provide functionality under particular conditions. more...
Organism:
Nostoc sp. PCC 7120 = FACHB-418
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29232
12 Samples
Download data: TSV
Series
Accession:
GSE159215
ID:
200159215
20.

Transcriptional response of Prochlorococcus strain MIT0604 to mitomycin C and UV stress

(Submitter supplied) Prochlorococcus genomes harbor a new type of mobile genetic elements named tycheposons. To study the effects on environmental stress on the gene expression and induction of tycheposons, we subjugated cultures of Prochlorococcus strain MIT0604 containing 7 such elements to treatments with mitomycin C and UV stress.
Organism:
Prochlorococcus sp. MIT 0604
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29975
9 Samples
Download data: CSV, TXT
Series
Accession:
GSE171435
ID:
200171435
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