GEO DataSets

(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) 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) Transcriptional profiling of Arabidopsis thaliana Ler wildtype and eid3 (empfindlicher im dunkelroten Licht 3) mutant seedlings in darkness and 45 min after a red-light pulse.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

12 Samples

Download data: TXT

(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) This experiment tests the effect of physiological dose of UV-B radiation on wild-type and uvr8-1 (UV Resistance Locus 8) and hy5-1 transcription factor mutants of Arabidopsis. Keywords: strain, stress response

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS1727

Platform:

GPL198

15 Samples

Download data

Analysis of leaves of UV resistance locus 8 uvr8-1 and transcription factor hy5-1 mutants following exposure to a physiological dose of UV-B. Results provide insight into the role of UVR8 and HY5 in the response to UV-B radiation and into the mechanisms of UV-B perception and signal transduction.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, transformed count, 3 genotype/variation, 2 stress sets

Platform:

GPL198

Series:

GSE3533

15 Samples

Download data

(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) DE-ETIOLATED1 (DET1) is a negative regulator of plant photomorphogenesis acting as a component of the C3D complex, which can further associate to CULLIN4 to form a CRL4C3D E3 ubiquitin ligase. CRL4C3D is thought to act together with CRL4COP1SPA ubiquitin ligase, to promote the ubiquitin-mediated degradation of the master regulatory transcription factor ELONGATED HYPOCOTYL5 (HY5), thereby controlling photomorphogenic gene regulatory networks. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28290 GPL21785

29 Samples

Download data: BW, TXT

(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) uORF-mediated translation reguration

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21785

8 Samples

Download data: TXT

(Submitter supplied) The mRNA expression profiles of the hypocotyl and root in WT and hy5 were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes were analyzed and compared within 22degC and 28degC and in different tissue type (hypocotyl vs root).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

24 Samples

Download data: TXT

(Submitter supplied) Rice transgenic plants of the bZIP encoding gene, OsbZIP48, in the Pusa Basmati 1 (PB1) variety have been found to display differences in the total height. In order to elucidate changes at the transcriptome level, microarray of the 10-day-old seedlings of over-expresseion (OE) and knock-down (KD) lines along with vector control (VC) were carried out.

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(Submitter supplied) Karrikins (KARs) are a class of butenolide molecules found in the smoke of burned plant material that can induce germination of many plant species that emerge after fire. Intriguingly, KAR perception is widely conserved and not limited to fire-followers. For example, germination of dormant Arabidopsis thaliana seeds can also be stimulated by KARs. Additionally, KAR treatment enhances responses of seedlings to light. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24025

9 Samples

Download data: TXT

(Submitter supplied) Nitrogen is major nutrient for plant growth. Two forms for inorganic nitrogen are available for plant, ammonium and nitrate. External status of them affects largely plant growth and production. Generally, root is a sole organ to uptake nitrogen. Hence, identifying regulatory genes depend on nitrogen status in roots is important to improve sustainable production or rice. To isolate the candidate gene, array experiments were performed. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

8 Samples

Download data: TXT, XLSX

(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 array

Platforms:

GPL198 GPL9062

18 Samples

Download data: BED, CEL

(Submitter supplied) FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

16 Samples

Download data: CEL