Pft1 glucose responses
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Michael Bevan
PROVIDER: E-MTAB-2297 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Arabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.
2011-05-18 | E-MEXP-2714 | biostudies-arrayexpress
Project description:The functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a. 2 organs X 3 treatments X 3 replicates This submission represnts ATH1 microarrays component of study.
2012-09-19 | E-GEOD-36789 | biostudies-arrayexpress
Project description:The establishment of ad/abaxial polarity is a fundamental event in plant development. It is critical for correct polar development of the leaf (the upper portion of the leaf is chloroplast rich and optimized for light capture while the lower portion is optimized for gas exchange) and for creating an environment that allows the formation of new meristems (centers of stem cell growth). Class III homeodomain-leucine zipper (HD-ZIPIII) proteins are conserved plant proteins that act as potent regulators of ad/abaxial polarity. HD-ZIPIII protein activity promotes the development of upper (adaxial) leaf fates and meristem formation; in its absence lower (abaxial) leaf fates develop and meristems fail to form. A network of regulatory factors controls the establishment of ad/abaxial leaf fates. However, this network is incomplete and how these factors control one another is poorly understood. Here we report a new family of plant genes, the LITTLE ZIPPER (ZPR) genes (consisting principally of a stretch of leucine zipper similar to the leucine zipper in HD-ZIPIII proteins) that are transcriptionally up-regulated by HD-ZIPIII activity. Furthermore, we show that the ZPR proteins interact with and repress HD-ZIPIII activity, thus forming a negative feedback loop. Our results suggest that HD-ZIPIII proteins exist in active homodimers and, together with the ZPR proteins, in inactive heterodimers. The newly discovered HD-ZIPIII/ZPR regulatory module would not only serve to dampen the effect of fluctuations in HD-ZIPIII protein levels but more importantly would provide a point of regulation - control over the ratio of inactive heterodimers to active homodimers - that could be influenced by other components of the pathway. For instance, the binding of a small hydrophobic molecule to the conserved (yet little understood) START domain present in the HD-ZIPIII proteins may influence the type of dimer formed. Published in:; Wenkel, S., Emery, J., Hou, B.-H., Evans, M.M.S. and M.K. Barton, 2007, A Feedback Regulatory Module Formed by LITTLE ZIPPER and HD-ZIPIII Genes. Plant Cell 2007 Experiment Overall Design: One of the five Arabidopsis HD-ZIPIII proteins, REVOLUTA, was placed under glucocorticoid control by fusing the glucocorticoid receptor (GR) domain to its amino terminus. This gene fusion was placed under the control of the highly and constitutively expressed viral CaMV35S promoter. Since the HD-ZIPIII genes are controlled by microRNAs, it was also necessary to introduce mutations that disrupted the microRNA complementary sequence. Transgenic Arabidopsis seedlings carrying this construct (GR-REV) as well as wild-type seedlings were grown in liquid culture for ten days. At this point, one flask each of wt and transgenic seedlings was treated with carrier alone (ethanol) and one flask each of wt and transgenic seedlings was treated with dexamethasone. RNA was harvested from these samples after one hour, labeled and hybridized to Affymetrix microarrays.
2008-06-15 | E-GEOD-7003 | biostudies-arrayexpress
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2007-07-13 | E-GEOD-3326 | biostudies-arrayexpress
Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 1: Growth conditions: Sterilized seeds will be stratified at 4degreeC for 3 days, exposed to white light for 2 h to induce germination, and grown on MS agar plates (0.9 % agar) without sugar in total darkness for 4 days at 22degreeC. Seedlings will then be transferred to the light conditions described for each slide below for 1 h (to identify early induced genes) and 4 hrs (maximum expression of the first initial light response of most target genes), respectively. All light treatments will be done in parallel to minimize the number of dark controls. All samples will be done in triplicate and only with shoots. Experimenter name = Thomas Kretsch; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment
2008-06-13 | E-GEOD-5617 | biostudies-arrayexpress
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Project description:To identify putative regulatory elements enriched in the promoters of target genes of the PGE-dependent retrograde signaling pathway, we analyzed 500 bp regions of sequence upstream of genes whose expression was down-regulated by lincomycin. We treated dark-grown Arabidopsis seedlings with lincomycin, sampled them before or after a short illumination and examined the genomic response using Affymetrix ATH1 oligonucleotide microarrays. Differentially regulated genes were ranked based on descending degree of significance (p-value) and the top 50 genes affected by lincomycin in dark grown seedlings and top 50 genes affected by the antibiotic after illumination were selected for further analysis. Experiment Overall Design: 2*2 factorial design, two variables are (1) with/without lincomycin treatment (2) with/without red illumination. There are 2 replicates for each condition.
2008-06-14 | E-GEOD-5759 | biostudies-arrayexpress
Project description:Arabidopsis thaliana AF7/ARF19 double knockout with ARF7 reintroduced under its own promotor with a glucocorticoid receptor added were treated with Auxin, Dexamethazone and cycloheximide to determine primary and secondary ARF7 auxin sensitive downstream targets
2015-04-01 | E-MTAB-3451 | biostudies-arrayexpress
Project description:Columbia (Col) seeds were sown on half-strength Murashige and Skoog (MS) medium, supplemented with 1% sucrose and 0.8% agar and grown vertically in culture room conditions. The 5-d-old homogenous seedlings were washed five times with sterile water and lastly with liquid half strength MS medium without sugar to remove residual exogenous sugar. In order to deplete internal sugars seedlings were grown in sugar free liquid half strength MS medium for 24 h in dark. Thereafter, the seedlings were treated with half-strength MS medium containing 0% G, 0% G + 1 uM BAP, 3% G, and 3% G + 1 uM BAP for 3 h in dark. RNA was extracted and microarray analysis was performed. Please note: G stands for glucose and BAP stands for 6-Benzylaminopurine (cytokinin)
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