Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of early response of Arabidopsis root tips exposed to 1 hour of red light

ABSTRACT: Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of roots exposed to 1 hour of red light. Early genes indicate elements involved in photomorphogenesis, chloroplast development, PAL pathways, root hair development are regulated by 1 hour of red light; We used microarrays to detail the gene expression underlying the effects of red light on roots. Experiment Overall Design: 7 Day dark-grown 1 cm Arabidopsis root tips were harvested for RNA extraction and hybridization on Affymetrix microarrays. We pooled samples from several Petri plates for each experiment to obtain enough RNA for arrays. Three experiments were performed. Treatment 1 hour of red light 630 nm (max) and dark controls

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Melanie Correll

PROVIDER: E-GEOD-4933 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Gene profiling of the red light signalling pathways in roots.

Molas Maria Lia ML Kiss John Z JZ Correll Melanie J MJ

Journal of experimental botany 20060814 12

Red light, acting through the phytochromes, controls numerous aspects of plant development. Many of the signal transduction elements downstream of the phytochromes have been identified in the aerial portions of the plant; however, very few elements in red-light signalling have been identified specifically for roots. Gene profiling studies using microarrays and quantitative Real-Time PCR were performed to characterize gene expression changes in roots of Arabidopsis seedlings exposed to 1 h of red ...[more]

PMID: 16908503

Similar Datasets

Transcription profiling of Arabidopsis dark 7-day-old Arabidopsis whole seedlings vs. 1h red light

Project description:Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of seedlings exposed to 1 hour of red light using a small sized sample of 5, 7-day-old seedlings and also performed dark controls. Methods that were developed for tissue extraction and labeling for microarrays were tested using these samples Experiment Overall Design: Only 5, 7 day-old dark-grown Arabidopsis seedlings were treated as described and harvested for RNA extraction and hybridization on Affymetrix microarrays. We pooled samples from one Petri plate with MS medium 2% sucrose. Treatment was 1 hour of red light 630 nm (max) and dark controls

2009-04-18 | E-GEOD-13383 | biostudies-arrayexpress

Transcription profiling of Arabidopsis SOL2 mutant root apex

Project description:Analysis of sol2 mutant. SOL2 protein is a receptor-like kinase; involved in CLE peptide signalling pathway. Results provide insignt into; the role of SOL2 in CLE signalling. Experiment Overall Design: GeneChip analyses were performed twice for comparison of gene expression in sol2 mutant and wild type plants.

2008-10-20 | E-GEOD-11119 | biostudies-arrayexpress

Expression data from 7 day old Arabidopsis roots with 1h Red light or dark

Project description:Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of roots exposed to 1 hour of red light. Early genes indicate elements involved in photomorphogenesis, chloroplast development, PAL pathways, root hair development are regulated by 1 hour of red light We used microarrays to detail the gene expression underlying the effects of red light on roots. Keywords: treatment

2006-08-15 | GSE4933 | GEO

Transcription profiling of Arabidopsis ahg1 and ahg3 mutants

Project description:The effect of ahg1 and ahg3 on the gene expression profiles is similar but some genes are differentially affected. Experiment Overall Design: To investigate the effect of ahg1 and ahg3 mutations, the genome wide gene expression profiles of germinating seedlings were examined. These mutations occurred in close but distinct PP2C genes. Stratified seeds were transferred to plates containing 0.5 uM ABA and allowed germinate at 23 Â°C under 16hr light 8hr dark conditions. After two days samples were collected for RNA extraction.

2008-06-15 | E-GEOD-6638 | biostudies-arrayexpress

Early effects of the photoperiodic induction of flowering on the root transcriptome.

Project description:The induction of flowering by the photoperiodic pathway (i.e. an increase in daylength) involves the production of systemic signals that induce the transition to reproductive development. In order to evaluate the early events occurring in the roots during the photoperiodic induction of flowering, we harvested the roots of 7 week-old Col-0 Arabidopsis thaliana plants grown plants exposed to a single 22-hour long day. Control plants were maintained under 8-hour short days. Plants were grown in hydroponics and roots tissues were harvested 16 and 22 hours after the beginning of the light period.

2016-06-30 | E-MTAB-4130 | biostudies-arrayexpress

Different gene expressions in root tips between CLE10 and CLE25 treatment

Project description:Cell–cell communication is critical for tissue and organ development. In plants, secretory CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides function as intercellular signaling molecules in various aspects of tissue development. However, little is known about intracellular signaling pathways functioning in vascular development downstream of the CLE ligands. To elucidate CLE signaling pathway, we performed GeneChip analysis. Arabidopsis roots were treated with chemically synthesized CLE10, or CLE25 at 1000 nM for 12 hours. Comparisons between CLE10 and CLE25 treatment will highlight the genes involved in the cause of different effects.

2010-09-03 | E-GEOD-19978 | biostudies-arrayexpress

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress

Transcription profiling time series of Cyanothece sp. grown in 12 hour light/12 hour dark then 24 h light

Project description:Cyanothece sp. ATCC 51142 12 hour light + 12 hour dark + 24 h light in a 48 hour time course

2008-07-11 | E-TABM-386 | biostudies-arrayexpress

Biophoton emission is involved in reactive oxygen species as well as mitochondrial proteins

Project description:Mitochondrial Proteomics under flooding stress in roots of soybean plants

2016-08-10 | PXD001477 | Pride

Transcription profiling of time series of Cyanothece sp. ATCC 51142 grown in 12 hour light/12 hour dark cycle

Project description:Cyanothece sp. ATCC 51142 12 hour light / 12 hour dark 48 hour time course

2008-07-11 | E-TABM-337 | biostudies-arrayexpress