GEO DataSets

(Submitter supplied) Circadian clocks are gene networks producing 24-h oscillations at the level of clock gene expression that is synchronized to environmental cycles via light signals. The ELONGATED HYPOCOTYL 5 (HY5) transcription factor is a signalling hub acting downstream of several photoreceptors and is a key regulator of photomorphogenesis. Here we describe a mechanism by which light quality could modulate the pace of the circadian clock through controlling abundance of HY5. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19580

7 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL8416 GPL9062

14 Samples

Download data: CEL, TXT

(Submitter supplied) LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology and defective hormonal and stimulus responses. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8416

12 Samples

Download data: CEL, TXT

(Submitter supplied) LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology and defective hormonal and stimulus responses. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

2 Samples

Download data: TXT

(Submitter supplied) To determine the functional relevance of the HY5 binding sites to the transcriptional regulation, we performed genome wide expression analysis using WT and hy5 grown in continuous white light for 4 days. Keywords: mutant/widetype comparative

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL988

4 Samples

Download data

(Submitter supplied) The transcription factor HY5 acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4656

4 Samples

Download data

(Submitter supplied) Seeds were germinated on 1/2 MS plates plus 1% sucrose and placed at 4°C for 3 days and then transferred to white light for 12 h before placed in blue light for another 4 days. Total RNA was extracted from samples including WT, agb1, cry1 cry2 and hy5 with RNAprep plant kit (TIANGEN), and followed by DNase I (Takara) treatment. This study reveals the molecular basis for light and G-protein crosstalk by analyzing gene expression profile under control of both signals.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: TXT

(Submitter supplied) To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

6 Samples

Download data: BED, TXT

(Submitter supplied) Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of ELIP1, ELIP2, APX2 and LHCB2.4 in the phyA, phyB, cry1 and cry2 photoreceptor mutants and hy5 and hyh transcription factor mutants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

21 Samples

Download data: CEL, CHP

(Submitter supplied) The transcriptional profiles of several genotypes of Arabidopsis seedling shoots were compared in dark and after 1 hr of monochromatic red-light treatment.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL10037

43 Samples

Download data: CEL

(Submitter supplied) ● Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SnRK1, a key mediator of responses to low energy. ● We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic, and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) The time between seed germination and the development of the first true leaves is crucial for plants success. Depending on the environmental light conditions a plant must decide which developmental program to use. If light is limited, the seedling will use etiolated growth characterized by an elongated hypocotyl and tightly-closed, underdeveloped cotyledons, thus allowing it to reach a light source as quickly as possible. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

28 Samples

Download data: CSV

(Submitter supplied) Transcription regulation requires many protein interactions on chromatin, and only a subset of transcription factors have well-defined activation or repression domains. The Arabidopsis transcription factor HY5 controls critical growth-related gene expression programs during plant development, but it’s primary activity in regulating transcription remains unclear. To address this question, we generated constitutive repressor and activator HY5 fusion proteins to direct the expression of HY5 target genes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

11 Samples

Download data: BEDGRAPH, XLSX

(Submitter supplied) Transcription regulation requires many protein interactions on chromatin, and only a subset of transcription factors have well-defined activation or repression domains. The Arabidopsis transcription factor HY5 controls critical growth-related gene expression programs during plant development, but it’s primary activity in regulating transcription remains unclear. To address this question, we generated constitutive repressor and activator HY5 fusion proteins to direct the expression of HY5 target genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

32 Samples

Download data: TXT

(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) 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) Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

64 Samples

Download data: TXT