GEO DataSets

(Submitter supplied) Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. more...

Organism:

Bacillus subtilis; Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24034 GPL21222 GPL24109

88 Samples

Download data: TXT

(Submitter supplied) Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

36 Samples

Download data: TXT

(Submitter supplied) Construction of a global gene co-expression network to determine gene relatedness and expand regulatory pathways in the model cyanobacterium Synechococcus 7002.

Organism:

Picosynechococcus sp. PCC 7002

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18074

8 Samples

Download data: TXT

(Submitter supplied) Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing the fast-growing response of Synechococcus sp. PCC 7002 response to variable irradience levels.

Organism:

Picosynechococcus sp. PCC 7002

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18074

6 Samples

Download data: TXT

(Submitter supplied) RNA Polymerase-II active regions were mapped comparing mouse neural retina tissue at age P25 and P2 to find novel gene activation predictions during maturation of photoreceptors. Over 800 predictions of increased activation were novel compared to previous mRNA expression array studies.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BED, CEL

(Submitter supplied) Forkhead box (FOX) transcription factors regulate a wide variety of cellular functions in higher eukaryotes, including cell cycle control and developmental regulation. In Saccharomyces cerevisiae, Forkhead proteins Fkh1 and Fkh2 perform analogous functions, regulating genes involved in cell cycle control, while also regulating matingtype silencing and switching involved in gamete development. Recently, we revealed a novel role for Fkh1 and Fkh2 in the regulation of replication origin initiation timing, which, like donor preference in mating-type switching, appears to involve long-range chromosomal interactions, suggesting roles for Fkh1 and Fkh2 in chromatin architecture and organization. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14887

30 Samples

Download data: PAIR

(Submitter supplied) Following divergence from Arabidopsis thaliana, Brassica rapa underwent a whole genome triplication followed by extensive genome fractionation. Preferential retention of circadian clock genes suggest that expansion of the circadian network may play an important role during B. rapa domestication. To characterize the circadian transcriptome network, RNA-seq was performed in the B. rapa oil-type variety R500 following photocycle and thermocycle circadian time courses. more...

Organism:

Brassica rapa subsp. trilocularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25920

96 Samples

Download data: CSV

(Submitter supplied) The temporal control of gene expression leads to time of day effects on metabolism and physiology. To identify early transcript level changes occurring in the Brassica rapa oil-type variety R500 during initial drought perception we performed an RNA-seq time course experiment. Leaf tissue was collected from well-watered and drought treated 18 day old plants grown under 14h light at 22°C/10h dark at 18°C every 4h over 2 days with 2 biological replicates at every time point. more...

Organism:

Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16440

48 Samples

Download data: TXT

(Submitter supplied) The gram-positive bacterium, Streptomyces avermitilis holds industrial importance, which produces widely used anthelmintic agent, avermectin. Furthermore, S. avermitilis is generally considered as a prominent heterologous gene expression host for diverse secondary metabolites biosynthesis. However, despite of its industrial importance, it largely remains unknown how its genome is organized and regulated for timely gene expression. more...

Organism:

Streptomyces avermitilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25453

22 Samples

Download data: TXT

(Submitter supplied) Gene regulation in mammals involves a complex interplay between promoter and distal regulatory elements that function in concert to drive precise spatio-temporal gene expression programs. However, the dynamics of distal gene regulatory elements and its function in transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here we use a combinatorial analysis of genomewide datasets for chromatin accessibility (FAIRE-Seq) and enhancer mark H3K27ac to reveal a highly dynamic nature of chromatin accessibility during neurogenesis that gets restricted to certain genomic regions as neurons acquire a post-mitotic, terminally differentiated state. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

20 Samples

Download data: TXT

(Submitter supplied) Although genome-wide transcriptional analysis has been used for many years to study bacterial gene expression, many aspects of the bacterial transcriptome remain undefined. A prominent example is antisense transcription, which has been observed in a number of bacteria, though the function of antisense transcripts, and their distribution across the bacterial genome, is still unclear. Single-stranded RNA-seq results revealed a widespread and non-random pattern of antisense transcription covering more than two-thirds of the B. more...

Organism:

Bacillus anthracis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15353

4 Samples

Download data: TXT

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

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

43 Samples

Download data: GPR, TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

9 Samples

Download data: GPR, TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

15 Samples

Download data: TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

8 Samples

Download data: TXT

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

20 Samples

Download data: GPR, TXT

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

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

25 Samples

Download data: GPR

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO2517::kan mutant strain (LY2517) and compare it to the wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

13 Samples

Download data: GPR

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO2517::kan mutant strain (LY2517) and compare it to the wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

12 Samples

Download data: GPR

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO6268::kan mutant strain (WL6268) and compare it to the wild-type M145 strain. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL4908

13 Samples

Download data: GPR