Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20055 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1887350.fastq.gz | Fastqsanger.gz | |||
| ERR1887360.fastq.gz | Fastqsanger.gz | |||
| ERR1887370.fastq.gz | Fastqsanger.gz | |||
| ERR1887380.fastq.gz | Fastqsanger.gz | |||
| ERR1887390.fastq.gz | Fastqsanger.gz |
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Project description:We used the phospho-TRAP protocol (Knight et al., 2011) to profile lateral septum populations that are activated following 1 hour of restraint stress.
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Project description:The sfr6 mutant was identified on the basis of its failure to cold acclimate, and exhibits a marked deficiency in cold-and osmotic stress-inducible gene expression (Knight et al., 1999). We have demonstrated that genes of this type (so-called COR genes) are misregulated if they contain the DRE (drought-responsive element, or CRT; C-repeat) cis acting element in their promoter (Boyce et al., 2003). Micro-array analysis has allowed us to identify a number of COR genes misregulated in sfr6, all of which contain the DRE element. However, these experiments have indicated that other genes, not of the COR group, are also misregulated in the mutant and these do not contain the DRE element. We chose the three non-COR genes that were most clearly down-regulated in sfr6 on our previous micro-array, and identified each as of these as dark-inducible. We now seek to address two questions: (1) Can we discover more dark-regulated genes that are down-regulated in the mutant, and thus identify a second cis-acting element with which SFR6 may be interacting? (2) Do all of the non-COR genes that are misregulated in sfr6 fall into the category of dark-inducible, or is SFR6 likely to be interacting with three or more regulons? For this micro-array experiment, we will subject sfr6 and wild type Arabidopsis, grown in a 16/8-h light/dark cycle, to darkness for 3h or 6h at ambient growth temperature. Under these conditions we see strong up-regulation of the three genes we have identified as dark-inducible, and we see clear down-regulation of expression in sfr6. References. Knight H, Veale E, Warren GJ, Knight MR (1999) The sfr6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE sequence motif. Plant Cell 11: 875-886. Boyce JM, Knight H, Deyholos M, Openshaw MR, Galbraith DW, Warren G, Knight MR (2003). The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stress. Plant Journal 34: 395-406. Experimenter name = Heather Knight Experimenter phone = 01865 275023 Experimenter fax = 01865 275074 Experimenter institute = University of Oxford Experimenter address = Department of Plant Sciences Experimenter address = University of Oxford Experimenter address = South Parks Road Experimenter address = Oxford Experimenter zip/postal_code = OX1 3RB Experimenter country = UK Keywords: growth_condition_design; genetic_modification_design
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Project description:The sfr6 mutant was identified on the basis of its failure to cold acclimate, and exhibits a marked deficiency in cold-and osmotic stress-inducible gene expression (Knight et al., 1999). We have demonstrated that genes of this type (so-called COR genes) are misregulated if they contain the DRE (drought-responsive element, or CRT; C-repeat) cis acting element in their promoter (Boyce et al., 2003). Micro-array analysis has allowed us to identify a number of COR genes misregulated in sfr6, all of which contain the DRE element. However, these experiments have indicated that other genes, not of the COR group, are also misregulated in the mutant and these do not contain the DRE element. We chose the three non-COR genes that were most clearly down-regulated in sfr6 on our previous micro-array, and identified each as of these as dark-inducible. We now seek to address two questions: (1) Can we discover more dark-regulated genes that are down-regulated in the mutant, and thus identify a second cis-acting element with which SFR6 may be interacting? (2) Do all of the non-COR genes that are misregulated in sfr6 fall into the category of dark-inducible, or is SFR6 likely to be interacting with three or more regulons?; For this micro-array experiment, we will subject sfr6 and wild type Arabidopsis, grown in a 16/8-h light/dark cycle, to darkness for 3h or 6h at ambient growth temperature. Under these conditions we see strong up-regulation of the three genes we have identified as dark-inducible, and we see clear down-regulation of expression in sfr6. References. Knight H, Veale E, Warren GJ, Knight MR (1999) The sfr6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE sequence motif. Plant Cell 11: 875-886. Boyce JM, Knight H, Deyholos M, Openshaw MR, Galbraith DW, Warren G, Knight MR (2003). The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stress. Plant Journal 34: 395-406. Experimenter name = Heather Knight; Experimenter phone = 01865 275023; Experimenter fax = 01865 275074; Experimenter institute = University of Oxford; Experimenter address = Department of Plant Sciences; Experimenter address = University of Oxford; Experimenter address = South Parks Road; Experimenter address = Oxford; Experimenter zip/postal_code = OX1 3RB; Experimenter country = UK Experiment Overall Design: 4 samples were used in this experiment
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Project description:We have been determining signalling components essential for heat tolerance in Arabidopsis thaliana (Larkindale, J., and Knight, M.R. (2002). Protection against heat stress-induced oxidative damage in Arabidopsis involves calcium, abscisic acid, ethylene, and salicylic acid. Plant Physiol 128, 682-695). We have most recently found that a heat-induced respiratory burst is necessary for tolerance to high temperatures in Arabidopsis (Larkindale, Torres, Jones and Knight, unpublished). We have observed that one of the Arabidopsis respiratory burst homologues, AtrbohB, is necessary for the generation of this AOS burst in response to heat, and consequently we have also found that an AtrbohB null mutant shows reduced tolerance to heating (Larkindale, Torres, Jones and Knight, unpublished). This mutant also shows reduced expression of genes from the HSP90 family (Evans, Larkindale and Knight, unpublished).This application is for transcriptomic analysis of the AtrbohB null mutant in response to heat, in order to understand which genes are activated as a result of heat-induced respiratory bursts in Arabidopsis and also which genes are necessary for physiological thermotolerance in Arabidopsis. The experiment will involve 6 samples (chips), 3 from wild type Columbia and 3 from the AtrbohB null mutant. Seedlings will be treated at 20, 30 and 40 degrees centigrade for 1 hour, RNA extracted and submitted to microarray analysis. One hour treatment has been shown to display clear differences in HSP90 expression and physiological damage, and the temperatures chosen because 30 degrees is a temperature at which acquired thermotolerance can be initiated (thus genes involved in this process can be monitored) and 40 degrees is a temperature at which we observe physiological damage, and gives good discrimination between mutant and wild type. Keywords: strain_or_line_design
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Project description:We have been determining signalling components essential for heat tolerance in Arabidopsis thaliana (Larkindale, J., and Knight, M.R. (2002). Protection against heat stress-induced oxidative damage in Arabidopsis involves calcium, abscisic acid, ethylene, and salicylic acid. Plant Physiol 128, 682-695). We have most recently found that a heat-induced respiratory burst is necessary for tolerance to high temperatures in Arabidopsis (Larkindale, Torres, Jones and Knight, unpublished). We have observed that one of the Arabidopsis respiratory burst homologues, AtrbohB, is necessary for the generation of this AOS burst in response to heat, and consequently we have also found that an AtrbohB null mutant shows reduced tolerance to heating (Larkindale, Torres, Jones and Knight, unpublished). This mutant also shows reduced expression of genes from the HSP90 family (Evans, Larkindale and Knight, unpublished).This application is for transcriptomic analysis of the AtrbohB null mutant in response to heat, in order to understand which genes are activated as a result of heat-induced respiratory bursts in Arabidopsis and also which genes are necessary for physiological thermotolerance in Arabidopsis. The experiment will involve 6 samples (chips), 3 from wild type Columbia and 3 from the AtrbohB null mutant. Seedlings will be treated at 20, 30 and 40 degrees centigrade for 1 hour, RNA extracted and submitted to microarray analysis. One hour treatment has been shown to display clear differences in HSP90 expression and physiological damage, and the temperatures chosen because 30 degrees is a temperature at which acquired thermotolerance can be initiated (thus genes involved in this process can be monitored) and 40 degrees is a temperature at which we observe physiological damage, and gives good discrimination between mutant and wild type.
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Project description:The sfr6 mutant was identified on the basis of its failure to cold acclimate, and exhibits a marked deficiency in cold-and osmotic stress-inducible gene expression (Knight et al., 1999). We have demonstrated that genes of this type (so-called COR genes) are misregulated if they contain the DRE (drought-responsive element, or CRT; C-repeat) cis acting element in their promoter (Boyce et al., 2003). Micro-array analysis has allowed us to identify a number of COR genes misregulated in sfr6, all of which contain the DRE element. However, these experiments have indicated that other genes, not of the COR group, are also misregulated in the mutant and these do not contain the DRE element. We chose the three non-COR genes that were most clearly down-regulated in sfr6 on our previous micro-array, and identified each as of these as dark-inducible. We now seek to address two questions: (1) Can we discover more dark-regulated genes that are down-regulated in the mutant, and thus identify a second cis-acting element with which SFR6 may be interacting? (2) Do all of the non-COR genes that are misregulated in sfr6 fall into the category of dark-inducible, or is SFR6 likely to be interacting with three or more regulons? For this micro-array experiment, we will subject sfr6 and wild type Arabidopsis, grown in a 16/8-h light/dark cycle, to darkness for 3h or 6h at ambient growth temperature. Under these conditions we see strong up-regulation of the three genes we have identified as dark-inducible, and we see clear down-regulation of expression in sfr6. References. Knight H, Veale E, Warren GJ, Knight MR (1999) The sfr6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE sequence motif. Plant Cell 11: 875-886. Boyce JM, Knight H, Deyholos M, Openshaw MR, Galbraith DW, Warren G, Knight MR (2003). The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stress. Plant Journal 34: 395-406.
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