Project description:Gene expression Arabidopsis 24h cold-treated, 4c, seedlings to identify a *gold-standard* set of cold-responsive transcripts. Most of the CBF overexpression lines are in WS, therefore, it is necessary to identify a consistent set of transcripts that are detectible as cold-induced on the ATH1 platform for both WS and Columbia, so that appropriate comparisons can be made to determine the effects of low temperature in CBF overexpressing or loss of function plants in a WS background and an attempt can be made to compare the results of altered CBF function to published microarray studies. We aimed to identify a set of *gold-standard* cold responsive transcripts that were induced in multiple different experiments performed by different researchers and were detectible in both the WS and Col-0 ecotypes. This series contributes the 24h cold-treated WS ecotypes, along with additional Col-0 cold-treated and control samples for normalization purposes. Keywords: Expression profiling by array
Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG
Project description:Nine accessions of Arabidopsis were sampled before and after 14d of cold acclimation at 4°C. Transcript data were combined with metabolite data and related to quantitative measurement of plant freezing tolerance as determined by leaf electrolyte leakage assays.
Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations.
Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series
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
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
Project description:To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 µM IAA. Keywords: Expression profilling by array
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. Experiment Overall Design: Two replicates for each time point of 0 hours, 3 hours, 6 hours and 24 hours of cold treatment for the wildtype (control) and ice1 (mutant).
Project description:Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories. We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1).