Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Light- and plastid-regulated transcriptomes in Arabidopsis seedlings

ABSTRACT: Plastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes. We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes. Our analyses provide evidence that light and plastid signaling are interactive processes and are consistent with these interactions serving as major drivers of chloroplast biogenesis and function. Four biological replicates were grown separately under the same conditions. Arabidopsis seedlings were grown in the presence (+Lin) or absence (-Lin) of lincomycin in 0.5 µmol m-2 s-1 blue plus red (BR) light for 6 days. After 6 days of growth in 0.5 µmol m-2 s-1 of BR light, seedlings were transferred to 60 µmol m-2 s-1 BR light. 50-100 seedlings were collected before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Michael Ruckle

PROVIDER: E-GEOD-24517 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of 6 day old shoots of 6 rice accessions under WL or WL + supplemental FR (far-red) light

Project description:This experiment was designed to uncover the transcriptomic changes that would occur in rice after 24 h of supplemental FR treatment, in an accession dependant manner. To do so, 6 different varieties of rice (IR64, Nipponbare, Luk Takhar, M Blatec, Mudgo, Sabharaj and Zhenshan) were grown in the greenhouse facilities of the Botanical Gardens, Utrecht University, in The Netherlands, in summer and autumn of 2021. After five days in WL (400 µmol m-2 s-1 of combined sunlight and artificial light), the treatment group was exposed to supplemental FR (500 µmol m-2 s-1 FR, R:FR of 0.2) light for 24 hours. The whole shoot was sampled, with four plants pooled in one sample. The experiment was repeated four times, resulting in 48 samples (6 varieties x 2 treatments x 4 replicates). Same samples were run on two individual lanes.

2024-04-24 | E-MTAB-13023 | biostudies-arrayexpress

RNA-seq of etiolated 9 day old maize seedling second leaves after exposure to either blue, red or no light conditions for three hours

Project description:Characterisation of the differences in transcript abundance between maize leaves that have been exposed to blue, red, or no light: B73 maize seeds were planted and grown in the dark for 9 days. Etiolated second leaves were clamped 5 cm from the leaf tip by a Licor 6800 device equipped with a multi-phase flash fluorometer head, which administered 100 µmol m-2s-1 of either 100% red or 100% blue light. The Licor was configured with flow rate 500 µmol s⁻¹, 400 µmol mol⁻¹ CO2, leaf temperature 28°C and 60% humidity. Fluorescence and gas exchange were measured every 15 minutes for 3 hours. Leaf samples were collected between 12.30am-2pm each day.

2019-06-10 | E-MTAB-7200 | biostudies-arrayexpress

Arabidopsis thaliana seedlings:early light regulated gene expression in Ler wildtype versus eid3 mutant

Project description: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. Arabidopsis thaliana Ler wildtype and eid3 mutant seedlings were grown on 1/2 MS Agar plates covered with filter paper for 4 days in darkness after induction of germination with 2 h red light. Samples were either treated with 2 min red light (30 µmol/m2s) or kept in darkness and harvested after additional 45 min in darkness. 3 biological replicas were used for each of the 4 experimental conditions.

2012-01-01 | E-GEOD-33856 | biostudies-arrayexpress

atmyc2_cop1_mutant_light_ABA_treatment

Project description:Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling Keywords: Light and abscisic acid treatment Expression data for wild-type, atmyc2, cop1-6, and atmyc2 cop1-6 seedlings under constant dark, blue-light and blue-light along with abscisic acid Ten-day-old Arabidopsis (wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant) seedlings grown under constant dark, constant blue-light (35 µmol/sec/m2), and constant blue-light along with ABA (0.5 µm) were used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.

2009-12-31 | E-GEOD-8955 | biostudies-arrayexpress

RNA-Seq data of Thalassiosira hyalina and Nitzschia frigida over a time course of high-light exposure under low and high pCO2

Project description:The diatoms Thalassiosira hyalina and Nitzschia frigida are important members of Arctic pelagic (open-water) and sympagic (ice-associated) microalgal communities. We investigated here the molecular mechanisms these algae apply to cope with abrupt high light exposure (Shift from 20 to 380 µmol photons m-2 s-1, resembling upwelling or ice break-up). Experiments were done under contemporary as well as future pCO2 (400 vs. 1000 µatm) to investigate whether [CO2] or pH modulate the reactions to high light intensities. After proper acclimation to the low-light regime, cells were sampled (= 0 hours), then exposed to the high-light treatment expression patterns were followed over 120h. Transcriptomic data were discussed also in the light of an accompanying physiological dataset from the same experiment (Ane Kvernvik et al. in prep).

2020-03-03 | E-MTAB-6999 | biostudies-arrayexpress

Saccharomyces cerevisiae transcriptome analysis of conditional yjr141w-psd mutant compared to control strain

Project description:The experiment investigates the consequences of Yjr141w downregulation on gene expression in yeast. The essential protein Yjr141w was depleted from cells using a tagged variant (Yjr141w-psd). The photo-sensitive degron (psd) module initiates degradation of the tag and its associated protein upon blue-light exposure. Altogether, we compared samples of the control yeast strain (ESM356-1) grown in darkness (3 arrays) and grown exposed to blue-light (wavelength 465 nm; light-flux 30 µmol m-2 s-1) with the Yjr141w-psd strain (YAL81) grown in darkness and grown exposed to blue-light.

2018-03-18 | E-MTAB-5022 | biostudies-arrayexpress

Light- and plastid-regulated transcriptomes in Arabidopsis seedlings

Project description:Plastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes. We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes. Our analyses provide evidence that light and plastid signaling are interactive processes and are consistent with these interactions serving as major drivers of chloroplast biogenesis and function.

2012-03-02 | GSE24517 | GEO

Microarray analysis of rosette leaf tissue for four-week-old Col-0 wild type, ugt76b1-1 knockout mutant and UGT76B1-OE overexpression Arabidopsis plants

Project description:This assay is designed for microarray measurements for 9 samples. In each sample, leaves from eight four-week-old Arabidopsis plants were harvested to be pooled. Three lines are included in this assay: Col-0, ugt76b1-1 and UGT76B1-OE. For each line, three biological replicates were designed. Plants were grown under a 14 h light/ 10 h dark regime at 45-60 µmol m-2 s-1 fluorescent light.

2024-08-01 | E-MTAB-13784 | biostudies-arrayexpress

Transcription profiling by array of Emiliania huxley haploid and diploid cells grown under different light treatments

Project description:Haploid (1N) and diploid (2N) cells of Emiliania huxley (RCC 1217/1216) were grown under 50 and 300 µmol photons m-2 s-1. Differential gene expression was assessed between the ploidy stages at same irradiance and between the light treatments of same strains.

2010-10-01 | E-MEXP-2896 | biostudies-arrayexpress

Molecular responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum

Project description:We have investigated both the response to prolonged darkness and the re-acclimation to “moderate intensity” white irradiance (E = 100 µmol m-2 s-1) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance.

2013-04-01 | GSE42039 | GEO

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