Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The roles of red light and phytochrome A/B in photomorphogenesis

ABSTRACT: Analysis of etiolated seedlings exposed for 1hr to red light. Phytochromes are red/far-red light receptors, palying important roles in photomorphogenesis. Results suggest that red light and phytochromes regulate a set of genes' expression in seedlings.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE111380 | GEO | 2021/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis

Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations

2010-05-01 | GSE19843 | GEO

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs.

2015-03-19 | GSE60835 | GEO

photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis

2010-04-30 | E-GEOD-19843 | biostudies-arrayexpress

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

2015-03-19 | E-GEOD-60835 | biostudies-arrayexpress

Expression profiles of dark or red-light treated WT and phytochrome mutants

Project description:The mRNA expression profiles of the wild type, phyB and phyAB mutants were analyzed with darkness or 1 hour red light treatment. Results provide insight into the role of red-light and phytochromes in gene expression.

2019-08-21 | GSE118824 | GEO

Expression data of Arabidopsis thaliana (Ler accession) phytochrome phyABCDE quintuple mutant and phyABDE quadruple mutant in response to red light, and their comparison to WT expression data

Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.

2012-04-01 | GSE31587 | GEO

SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.

2017-08-10 | GSE85883 | GEO

P-body mediated translational control in photomorphogenesis

Project description:Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.

2019-06-20 | GSE107892 | GEO

The roles of red light and phytochrome A/B in photomorphogenesis

Project description:The roles of red light and phytochrome A/B in photomorphogenesis

| PRJNA436745 | ENA

mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID: .

2012-05-08 | GSE36274 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data