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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data of Col:LUC Arabidopsis treated with antimycin A (AA) in the presence or absence of a synthetic auxin analogue

ABSTRACT: Mitochondrial stress stimuli such as AA caused a transient suppression of auxin signaling and conversely, auxin treatment represses a part of the response to AA treatment. Expression data of Col:LUC Arabidopsis treated with antimycin A (AA) in the presence or absence of a synthetic auxin analogue Total RNA extraction was carried out on 80 mg of Col:LUC Arabidopsis seedlings grown on B5 media for 10 days and transferred to fresh plates, containing either B5 media or B5 media supplemented with 4.5 µM NAA for an additional 3 days. Seedlings were treated with 50 µM AA for 3 hours.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Simon Law

PROVIDER: E-GEOD-57140 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A Functional Antagonistic Relationship between Auxin and Mitochondrial Retrograde Signaling Regulates Alternative Oxidase1a Expression in Arabidopsis.

Ivanova Aneta A Law Simon R SR Narsai Reena R Duncan Owen O Lee Jae-Hoon JH Zhang Botao B Van Aken Olivier O Radomiljac Jordan D JD van der Merwe Margaretha M Yi KeKe K Whelan James J

Plant physiology 20140512 3

The perception and integration of stress stimuli with that of mitochondrion function are important during periods of perturbed cellular homeostasis. In a continuous effort to delineate these mitochondrial/stress-interacting networks, forward genetic screens using the mitochondrial stress response marker alternative oxidase 1a (AOX1a) provide a useful molecular tool to identify and characterize regulators of mitochondrial stress signaling (referred to as regulators of alternative oxidase 1a [RAOs ...[more]

PMID: 24820025

Similar Datasets

Expression data of Col:LUC Arabidopsis treated with antimycin A (AA) in the presence or absence of a synthetic auxin analogue

Project description:Mitochondrial stress stimuli such as AA caused a transient suppression of auxin signaling and conversely, auxin treatment represses a part of the response to AA treatment. Expression data of Col:LUC Arabidopsis treated with antimycin A (AA) in the presence or absence of a synthetic auxin analogue

2014-06-01 | GSE57140 | GEO

Transcription profiling of grapevine cell culture treated with methyly jasmonate, salicylic acids and ethanol controls

Project description:Calli generated from grape berries were used to establish a cell suspension in Gamborgs B5 liquid medium with minimal organics supplemented with 30 gL-1 sucrose, 0.25 gL-1 casein hydrolysate, 0.93 ?M kinetin and 0.54 ?M naphthaleneacetic acid (NAA) and incubated in darkness at 26°C. <br>The cells were cultured in 250 mL flasks (50 mL of cell suspension in each) incubated in darkness on an orbital shaker at 100 rpm. The cell suspensions were sub-cultured every 2 weeks using an initial packed cell volume (PCV) of 15%. For the evaluation of the effect of elicitor addition on the changes in gene expression, 100 mL flasks containing 20 mL of the above cell suspension were used. Each treatment was conducted in triplicate.<br><br>In a set of preliminary experiments studying the effect of elicitors on the volatiles produced by the cell suspensions, the compounds were added during the exponential growth phase when the PCV was approximately 50%. After 72h incubation in darkness after elicitor addiction, cells were harvested. The elicitors screened for their ability to induce volatile compound production were: 500 µM methyl jasmonate (MeJA); 500 uM MeJA + 500 µM salicylic acid (SA); 500 µM jasmonic acid (JA). Controls were conducted by adding the same volume of the solvent used to dissolve each elicitor to the cultures. For the jasmonate and SA experiments the solvent was ethanol.<br>

2009-04-28 | E-MEXP-1524 | biostudies-arrayexpress

Transcription profiling of Arabidopsis cells cultures undergoing transdifferentiation

Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Experiment Overall Design: 6 samples

2008-06-14 | E-GEOD-6148 | biostudies-arrayexpress

Fatty Acid Binding Protein 5 is a Novel Target in Multiple Myeloma

Project description:To identify protein changes in human myeloma cancer cells resulting from FABP inhibition, we treated GFP+/Luc+MM.1S cells with the single inhibitors (50 µM BMS309405 or 50 µM SBFI-26) or the combination (50 µM of each) for 48 hour, isolated total cell proteins, and performed a mass spectrometry-based proteomic analysis.

2023-01-12 | PXD032829 | Pride

AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions

Project description:Samples-WT Basal condition primary cortex cells; WT B27 Starved-Primary cortex cells starved overnight without B27 supplement media. WT AA Starved-Primary cortex cell starved without amino acid for 2 hours. WT AA Refed-Primary cortex cell refed for 1 hour after amino acid starvation. KO Basal-SLC38 Knockout Primary cortex cells starved overnight without B27 supplement media. KO B27 Starved-SLC38 Knockout Primary cortex cell starved without amino acid for 2 hours. KO AA starved-SLC38 Knockout Primary cortex cell refed for 1 hour after amino acid starvation. KO AA Refed-SLC38 Knockout Primary cortex cell refed for 1 hour after amino acid starvation.

2021-06-03 | E-MTAB-10413 | biostudies-arrayexpress

The effect of sucrose and sulfamethoxazole on the Arabidopsis transcriptome

Project description:A chemical screen was performed in search of compounds that modify plant responses to sucrose. This screen uncovered that sulfamethoxazole (SMX), a folate biosynthesis inhibitor, acted synergistically with sucrose to inhibit hypocotyl elongation, suggesting interaction between these two pathways. Transcriptome analysis was performed to identify changes in transcript abundance that may underpin crosstalk between sucrose and SMX. Three-day-old dark-grown seedlings were treated to sucrose and SMX at concentrations that induced no change in hypocotyl elongation when administered independently, yet restricted elongation when both were present in the growth media (10mM and 0.2µM, respectively). This analysis uncovered multiple core auxin signalling components that exhibit altered transcript abundance in response to co-treatment with sucrose and SMX, suggesting that auxin signalling mediates crosstalk between these two pathways. This study highlights an input through which metabolic status can shape plant growth and development through hormone signalling. 12 arrays total. Three arrays as non-treated control, three arrays from seedlings raised in presence of 0.2µM SMX, three arrays from seedlings raised in presence of 10mM sucrose, and three arrays from seeldings raised in presence of both 10mM sucrose and 0.2µM SMX. Three biological replicates were produced for each growth treatment.

2013-06-30 | E-GEOD-37484 | biostudies-arrayexpress

An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance [seq]

Project description:Algal discs were transferred to a 12-well plate containing 2 ml liquid 0.5 Gamborg’s B5 mock or OPDA 25 µM, incubated for 2 hours on a shaker (120 rpm) and then the algae were frozen in liquid nitrogen and ground to a fine powder.

2020-03-04 | GSE141417 | GEO

Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis. differential gene expression analysis at 9 time-points/stages during somatic embryogenesis in cotton by deep sequencing, using Illumina GAIIx.

2012-05-31 | E-GEOD-38209 | biostudies-arrayexpress

Transcription factor transcriptome during somatic embryogenesis (SE) in Arabidopsis thaliana

Project description:To identify transcription factor (TF) genes exhibiting preferential expression during SE, expression profiles of 1,880 TFs were compared in two genotypes with largely different capacities for SE induction in IZE culture on auxin medium, namely the highly embryonic Col-0 accession and the tanmei mutant unable to form somatic embryos. Our study revealed 729 TFs whose expression changes during the 10-day incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. This study provides comprehensive data focused on the expression of TF genes during SE and provides guidelines for further research on functional genomics of SE. The experiment was designed to monitor the expression of 1,880 TF genes at three distinctive stages of IZE-derived embryogenic culture, which refer to: (i) freshly isolated explants competent to undergo embryogenic transition (0 d), (ii) explant tissue subjected to SE induction (5 d), and (iii) the advanced phase of embryogenesis related to somatic embryo formation (10 d).

2013-07-31 | E-GEOD-45697 | biostudies-arrayexpress

Auxin stimulates brassinosteroid biosynthesis in Arabidopsis roots

Project description:We found that auxin stimulates gene expression of DWF4, which encodes a rate-dertermining step in brassinosteroid biosynthesis pathways. This increased gene expressioin subsequently led to elevation of the biosynthetic flux in Arabidopsis roots. To determine the list of genes that are regulated by auxin-synthesizing brassinosteroids, we challenged Arabidopsis seedlings with either auxin only or auxin plus brassinosteroid biosynthetic inhibitor brassinazole. Keywords: Hormone treatment Arabidopsis seedlings (Columbia ecotype) were grown for 10 d on 1× MS agar-solidified media under long-day conditions (16:8, white light and dark cycle). The seedlings were then transferred to 2 different liquid media containing either 10–7 M 2,4-D or 10–7 M 2,4-D plus 10–6 M brassinazole. After 8 h of treatment, the seedlings were blotted with paper towels to remove excess media and subject to total RNA isolation. Total RNAs isolated from each batch were prepared from 3 replicate seedlings using an RNeasy plant mini kit (Qiagen, Germany).

2011-02-15 | E-GEOD-12964 | biostudies-arrayexpress

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