Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photoreceptor control of shoot meristem activity and leaf initiation

ABSTRACT: When Arabidopsis seedlings are grown in the dark, their shoot meristem remains in a repressed state and does not develop leaves. The tight control of leaf development by light provides the opportunity to analyse a fundamental plant developmental process in its very early stages. We have observed that activation of photoreceptors in dark-grown seedlings leads to a rapid and dramatic increase in mitotic activity in and around the shoot meristem. Cotyledons also exhibit an induction of cell cycle activity by light, but this consists of endoreduplication and occurs later. Many other processes take place upon induction by light, including the development of the photosynthetic apparatus and the synthesis of sunscreens, but these processes are expected to take place in both the leaf primordia and the cotyledons. We have used this information to carry out a whole transcriptome analysis of shoot meristem activation and early stages of leaf development by light. For this we dissected the shoot apical regions from seedlings grown in the dark or 1, 2, 6, 24, 48 or 72 h after transfer to light. We also dissected cotyledons from equivalent seedlings grown in the dark or 1 or 6 h after transfer to light. From these samples we obtained RNA used for hybridisations against the ATH1 GenChip. 16 samples were used in this experiment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Enrique Lopez-Juez

PROVIDER: E-GEOD-19261 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

BBX32 Role in Early Light Signaling in Arabidopsis

Project description:The transcriptional profiles of several genotypes of Arabidopsis seedling shoots were compared in dark and after 1 hr of monochromatic red-light treatment. The transcriptional profiles of several genotypes of Arabidopsis seedling shoots were compared in dark and after 1 hr of monochromatic red-light treatment.

2011-06-30 | E-GEOD-21174 | biostudies-arrayexpress

Ethylene treated Arabidopsis roots

Project description:Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia) stress. The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced metabolic hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of primary Arabidopsis thaliana root tips.

2022-12-19 | PXD031138 | Pride

RNAseq of wt and receptor mutant lines in response to 7 elicitor treatments over a 6-point time course

Project description:The degree to which plants discriminate among elicitors in early transcriptional responses is unknown. To test this, we selected a panel of seven elicitors recognized by the model plant Arabidopsis thaliana. Two-week old Arabidopsis seedlings in liquid culture were treated with each elicitor individually, and tissue flash-frozen at 0, 5, 10, 30, 90, and 180 min post-treatment. As a control, receptor mutants for each elicitor were treated and harvested in parallel with wt plants. The experiment was repeated four times. mRNA was extracted via pulldown of poly-A tail from bulk lysate, and libraries were prepared via tagmentation with custom Tn-5 adapter oligos. Libraries for each experiment were pooled, and sequenced across 2-3 flowcells of a NextSeq500 benchtop sequencer.

2021-01-29 | E-MTAB-9694 | biostudies-arrayexpress

Genome wide identification of ORE1 early target genes

Project description:Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts To identify genes more rapidly responding to elevated ORE1 expression we here repeated the previous experiment (Balazadeh et al., 2010), but shortened the EST induction time to 2 h (ORE1-IOE-2h dataset). Furthermore, to exclude potential misinterpretation due to EST treatment we also included an experiment where we transiently expressed a 35S::ORE1 construct in Arabidopsis mesophyll cell protoplasts and extracted RNA 6 h after the transfection (35S::ORE1-6h dataset);

2013-01-01 | E-GEOD-37536 | biostudies-arrayexpress

Genome wide identification of SHYG early target genes

Project description:Global transcriptome patterns were performed using SHYG-IOE-5h (5h after Estradiol and Mock treatment) To identify genes more rapidly responding to elevated SHYG , we perfromed gene expression profiling (Affymetrix) upon 5h Est treatment of SHYG-IOE plants.

2013-12-29 | E-GEOD-38721 | biostudies-arrayexpress

Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

Project description:Global transcriptome patterns were obtained from ATAF1-IOE seedlings at 1 h, 2 h and 5 h after estradiol induction or mock treatment, and from mature ATAF1-IOE leaves at 5 h after estradiol induction or mock treatment. To identify genes rapidly responding to elevated ATAF1 expression estradiol induction experiments were performed on ATAF1-IOE seedlings after 1 h, 2 h and 5 h of ATAF1 induction. In addition, expression profiles were obtained from mature leaves after 5 h of ATAF1 induction.

2014-08-30 | E-GEOD-54676 | biostudies-arrayexpress

Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. We performed whole-genome transcriptome (mRNA-seq) analysis on 5-day-old Arabidopsis thaliana Columbia wild-type (WT) and pif4pif5 seedlings exposed to low blue-light (LBL) or mock-treated for 1, 6 and 24 hours. In addition we performed mRNA-seq on WT, 35S::PIF4-9xMyc-6x-His-3xFlag(Flash) and 35S::PIF5-9xMyc-6x-His-3xFlag (Flash) seedlings treated with LBL or mock-treated for 16 hours.

2015-12-31 | E-GEOD-59699 | biostudies-arrayexpress

Transcription profiling of Arabidopsis seedlings overexpressing ERF6, a transcription factor of the ethylene response factor family

Project description:Microarray analyses were performed on Arabidopsis thaliana plants overexpressing ERF6. In this way it was hoped that any changes in the Arabidopsis transcriptome caused by overexpression would provide clues as to the role this gene plays in vivo.<br>Arabidopsis thaliana plants were transformed with 35S::ERF6 or the empty vector pK2GW7 (used as a control). Total RNA was extracted from untreated 10-day old seedlings. Three separate arrays were performed (the RNA for each slide having been extracted from an independent biological replicate).

2010-12-31 | E-MTAB-435 | biostudies-arrayexpress

Transcription profiling of wild type and cli186 mutant Arabidopsis seedlings grown with and without carbon and light to provide information about gene networks regulated by the interaction of light and carbon signaling pathways

Project description:This microarray experiment serves to identify the genes in the Arabidopsis genome that are regulated by carbon and light signaling interactions in 7 day dark grown seedlings. The expression profile of wild-type will be compared to the cli186 mutant, a mutant defective in carbon and light signaling. Plants of both the wild-type and cli186 genotypes are treated with the following light (L) and carbon (C) treatments: -C-L, +C-L, +C+L, -C+L. Comparison of the expression profiles under all treatments will help to identify genes that are misregulated in carbon and/or light treatments in the cli186 mutant.

2008-02-23 | E-MEXP-1112 | biostudies-arrayexpress

Arabidopsis inflorescence stems: upper flanks vs lower flanks after gravi-stimulation at 10 min and 30 min

Project description:Transcriptional profiling of upper flanks and lower flanks of Arabidopsis inflorescence stems after gravistimulation. Candidate genes which were up-regulated in the lower flanks relative to the upper falanks after gravi-stimulation at 30 min were identified. Two time-points experiments, at 10 min and 30 min. Biological replicates: 2 replicates for each experiments (as color swapped data)

2014-06-12 | E-GEOD-58417 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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