Arabidopsis cold transcriptome
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ABSTRACT:
PROVIDER: PRJEB19974 | ENA |
REPOSITORIES: ENA
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Project description:Arabidopsis thaliana phyllosphere time course
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Project description:To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades. In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of wild type and ice1, a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress conditions, but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1, and thus will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance. Keywords: Cold Stress response
2005-10-01 | GSE3326 | GEO
Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to cold for two widely used Arabidopsis thaliana ecotypes, C24 and Columbia (Col). Two Arabidopsis genotypes were grown in 1/2 MS plate. Forteen-day-old seedlings were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and cold treatment combination.
2012-12-01 | E-GEOD-37130 | biostudies-arrayexpress
Project description:Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Keywords: SAGE; time course; stress response; cold acclimation; freezing tolerance SAGE libraries were generated from A. thaliana leaf tissue collected after exposure to low temperature (4°C) for 0 minutes, 30 minutes, 2 hours, 2 days and one week, the tags were matched to the Arabidopsis genome and statistical analysis was performed to reveal differential gene expression.
2008-10-01 | E-GEOD-11461 | biostudies-arrayexpress
Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to cold for two widely used Arabidopsis thaliana ecotypes, C24 and Columbia (Col).
2012-12-01 | GSE37130 | GEO
Project description:Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Keywords: SAGE; time course; stress response; cold acclimation; freezing tolerance
2008-10-01 | GSE11461 | GEO
Project description:Time-course transcriptome data of Arabidopsis thaliana in LL condition
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Project description:time course uranyl nitrate response-Transcriptomic analysis of uranyl response in Arabidopsis thaliana
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Project description:Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. Expression patterns were compared between treatments, accessions and species.
2018-01-01 | GSE100108 | GEO
Project description:TabZIP6 is a Subgroup C bZIP protein from wheat. Some evidences have shown that TabZIP6 is involved in cold stress response. To elucidate the regulatory mechanism of TabZIP6 in plant cold response, cold treated/untreated TabZIP6-overexpressing Arabidopsis seedlings were used to perform microarray analysis.
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