GEO DataSets

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

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

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

Platform:

GPL17750

97 Samples

Download data

(Submitter supplied) We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17750

60 Samples

Download data: XLSX

(Submitter supplied) We used ChIP sequencing to measure genome-wide binding of transcription factors in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the rapid changes in light intensity that accompany changes in shading. Our analysis reveals that rapid changes in light intensity modulate the binding of RNA polymerase (RNAP) upstream of genes in a way that correlates with changes in downstream gene expression, suggesting that changes in transcriptional regulation control light-responsive gene expression changes. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17750

37 Samples

Download data: XLSX

(Submitter supplied) The goal of the experiment was to obtain a replicate of the wild-type LL circadian timecourse published in Vijayan et al, PNAS 106: 22564-22568 (2009), in order to identify reproducible circadian genes in LL.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

7 Samples

Download data: GPR

(Submitter supplied) The cyanobacterium Synechococcus elongatus contains a circadian clock which coordinates circadian changes in gene expression of a large percentage of its genes. The response regulator RpaA has been implicated as an important regulator of many circadian genes, but the role of this protein in regulating changes in gene expression genome-wide is not known. We show that deletion of rpaA abrogates circadian gene expression genome-wide and arrests cells in a gene expression state highly similar to that of wildtype cells in the morning. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17750

18 Samples

Download data: TXT

(Submitter supplied) The response regulator RpaA is required for control of genome-wide gene expression by the cyanobacterial circadian clock. RpaA is predicted to be a DNA binding protein based on sequence homology, but prior studies have been unable to detect binding in vitro or in vivo to a small panel of promoters. We used ChIP-Seq to determine whether RpaA associates with DNA in vivo, and if so, with what dynamics. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16957 GPL17750 GPL13530

19 Samples

Download data: WIG

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

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

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

4 related Platforms

108 Samples

Download data: GPR, WIG

(Submitter supplied) The goal of this experiment was to determine whether global circadian gene expression oscillation depends strictly on the presence of rpaA, even when the KaiABC post-translational oscillator is oscillating with a circadian period. Strains deleted for rpaA lack functional KaiABC post-translational oscillators because their reduced kaiBC expression level leads to a non-permissive Kai protein stoichiometry. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

49 Samples

Download data: GPR

(Submitter supplied) The goal of the experiment was to determine the difference in gene expression between the wild-type strain and a strain lacking rpaA (ΔrpaA). Because gene expression is not at steady-state in the wild-type -- it oscillates with a circadian period -- and we did not know a priori whether it is at steady-state in the ΔrpaA strain, we compared the time-averaged gene expression in the wild-type to the time-averaged gene expression in the ΔrpaA strain.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

2 Samples

Download data: GPR, TXT

(Submitter supplied) The goal of the experiment was to determine whether gene expression oscillates in the absence of rpaA. It was reported previously (e.g., Takai et al, PNAS 2006) that activity of a handful of individual expression reporters was arrythmic, and we conducted this microarray timecourse to determine whether expression is arrhythmic geneome-wide.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

13 Samples

Download data: GPR

(Submitter supplied) The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect. We performed RNA-seq experiment using the rpaA- “clock rescue” and “clock rescue” strains and we show that the rpaA- “clock rescue” strain is defective in transcription of genes crucial for utilization of carbohydrate stores at night.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

24 Samples

Download data: XLS

(Submitter supplied) The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-hour periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive – neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here we show that the topological status of the chromosome is highly correlated with circadian gene expression state. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

23 Samples

Download data: GPR

(Submitter supplied) In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, dramatically reduces the transcription rate in the dark (dark repression), and its cellular functions enormously depend on light as an energy source through photosynthetic activity. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression when illuminated or dark-acclimated cells are treated with photosynthesis inhibitors DCMU or DBMIB. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805; Synechococcus elongatus PCC 6301

Type:

Expression profiling by array

Platform:

GPL8012

28 Samples

Download data: CEL

(Submitter supplied) In this study, we implemented RNA sequencing to identify melatonin sensitive transcripts during culture maturation. This work demonstrates that majority of melatonin sensitive genes are growth stage specific. Melatonin caused differential gene expression of 81 transcripts during the exponential growth and 30 during early stationary phase. This indole molecule affects genes related to the biofilm formation, fimbria biogenesis, transcriptional regulators, carbohydrate transport and metabolism, phosphotransferase system (PTS), stress response, metal ion binding and transport. more...

Organism:

Klebsiella aerogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30003

12 Samples

Download data: TXT