GEO DataSets

(Submitter supplied) The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey of differential expression with a focus on antisense (as)RNAs and non-coding (nc)RNAs. A microarray was constucted with on average 5 probes for each transcript known thus far, including ncRNAs and asRNAs. The resulting 20,431 individual probes are duplicated on the array (Agilent 4x44k custom array) representing a technical replicate. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array; Non-coding RNA profiling by array

Dataset:

GDS3744

Platform:

GPL8567

12 Samples

Download data: TXT

(Submitter supplied) The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platform:

GPL8071

4 Samples

Download data: TXT

Analysis of cyanobacterium cultures subjected to various stressful growth conditions: CO2 depletion, dark, and high light. Results provide insight into molecular mechanisms, including antisense (as)RNAs and non-coding (nc)RNAs, underlying cyanobacteria adaptation to various stresses.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array, count, 4 stress sets

Platform:

GPL8567

Series:

GSE16162

12 Samples

Download data: TXT

(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

(Submitter supplied) We investigated Synechocystis high-density microarray data of three high-resolution time-series experiments with alternating light/dark rhythm, transition to continuous light, and transition to continuous darkness. Using ‘least oscillating set’ normalization and a clustering approach we found a daily temporal program for rhythmic expression of protein-coding and non-coding genes under light/dark conditions. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

62 Samples

Download data: TXT

(Submitter supplied) The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model system for studying biochemistry, genetics and molecular biology of photobiological processes. Despite its importance in basic and applied research, the genome-wide picture of transcriptional regulation in this bacterium is limited. Characteristic transcriptional responses to changes in the growth environment are expected to provide a scaffold for describing the Synechocystis transcriptional regulatory network as well as efficient means for functional annotation of genes in the genome. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Dataset:

GDS3745

Platform:

GPL7016

27 Samples

Download data: GPR

Analysis of cyanobacterium cultures grown under sulfur starvation conditions for up to 72 hrs. During S limitation, production of hydrogen, a clean and sustainable energy carrier, increases substantially. Results provide insight into gene expression changes during the transition to S starvation.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array, log2 ratio, 3 stress, 11 time sets

Platform:

GPL7016

Series:

GSE11970

27 Samples

Download data: GPR

(Submitter supplied) Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts. To date, such studies have investigated primarily Bacteria. more...

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18473

5 Samples

Download data: WIG

(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

(Submitter supplied) Carbohydrate metabolism is a tightly regulated process in photosynthetic organisms. The ability to utilize glucose for growth and to regulate storage carbohydrate (i.e. glycogen) metabolisms requires a number of regulatory elements. In the cyanobacterium Synechocystis sp. PCC 6803, the photomixotrophic growth protein A (PmgA), a putative serine/threonine kinase, is involved in governing these abilities; however its downstream regulatory elements are not well studied. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

5 Samples

Download data: TXT

(Submitter supplied) We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O2 concentration (bubbled with 99.9% N2/0.1% CO2). Significant transcriptional changes upon low O2 incubation included up-regulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31. This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and on plasmid pSYSX. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL11088

12 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) 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

(Submitter supplied) The direct photosynthetic production of polyhydroxyalkanoate in cyanobacteria was improved by increasing carbon flux to biosynthetic pathway and introducing enzyme with higher activity. To understand the global transcriptional changes under photoautotrophic PHA biosynthesis conditions, RNA-seq analysis was performed.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17697

6 Samples

Download data: TXT

(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

(Submitter supplied) In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

22 Samples

Download data: WIG

(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

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

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array; Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platforms:

GPL7821 GPL7822

295 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array

Platform:

GPL7822

252 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platform:

GPL7821

43 Samples

Download data