GEO DataSets

(Submitter supplied) The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11221 GPL9302

7 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) LHY and CCA1 encode single MYB transcription factors, involved in circadian clock. However, direct target genes of LHY and CCA1 in a genomic scale were largely unknown. To reveal bound genes by CCA1, chimeric protein CCA1-FLAG was expressed under CCA1 promoter in cca1 lhy (CCA1pro:CCA1-FLAG/ cca1 lhy). ChIP was performed using anti-FLAG antibody (F3165; SIGMA), which was bound to Dynabeads Protein G (100-03D; Life Technologies), and ChIP DNA were analyzed by IonPGM or Illumina GAII.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9302 GPL19056

2 Samples

Download data: BED

(Submitter supplied) We identified genome-wide PRR9 targets by conducting chromatin immunoprecipitation followed by high-throughput sequencing.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL17639

4 Samples

Download data: BED, TXT, XLS

(Submitter supplied) we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

48 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify the targets of RVE8, a MYB-like transcription factor involved in the circadian clock in Arabidopsis. Analysis of 7 days old rve8-1 RVE8::RVE8:GR and rve8-1 seedlings treated with dexamethasone or mock identified genes responsive to RVE8 induction.The RVE8 up-regulated genes are enriched for evening-phased genes while the down-regulated genes are enriched for a morning phase. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

96 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

36 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

36 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) The red-light regulated transcription factors FHY3 and FAR1 form a key point of light input to the plant circadian clock in positively regulating expression of genes within the central clock. However, the fhy3 mutant shows an additional red light-specific disruption of rhythmicity which is inconsistent with this role. Here we demonstrate that only fhy3 and not far1 mutants show this red specific disruption of rhythmicity. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

21 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) The goal of this study is to identify genes regulated by GRF1 and GRF3. Results: 2,596 and 2,212 differentially expressed genes were identified in the 35S:GRF1 and 35S:GRF3 plants, respectively, when compared with the grf1/grf2/grf3 triple mutant at a false discovery rate (FDR) of 0.05. Similarly, a set of 826 genes was identified as differentially expressed in the grf1/grf2/grf3 mutant when compared with the wild-type WS plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify direct target of GRF1 and GRF3.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

9 Samples

Download data: NARROWPEAK

(Submitter supplied) The biological functions of circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits are poorly understood. Here, we characterize the core clock gene CCA1 homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns which are positively regulated by rhythmic histone modifications (H3K4me3, H3K9ac and H3k36me3). more...

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

4 Samples

Download data: BED

(Submitter supplied) Members of the PIF quartet (PIFq) (PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. The objective of this genomic analysis was to define a comprehensive set of SD-regulated genes at dawn compared to free-running (LL) conditions in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17416

12 Samples

Download data: CEL, CHP

(Submitter supplied) Dynamic regulation of gene expression via signal transduction pathways is of fundamental importance during many biological processes such as cell state transitioning, cell cycle progression and stress responses. In this study we used serum stimulation as a cell response paradigm to apply the nascent RNA Bru-seq technique in order to capture early dynamic changes in the nascent transcriptome. Our data provides an unprecedented view of the dynamics of genome- wide transcription during the first two hours of serum stimulation in human fibroblasts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: BED