Arabidopsis thaliana strain:T87
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REPOSITORIES: ENA
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Project description:Genome-wide analysis of degradation sites in Arabidopsis T87 cultured cell
| PRJDB5913 | ENA
Project description:Ribosome profiling in Arabidopsis T87 cultured cell
| PRJDB10544 | ENA
Project description:Long-read sequencing using Arabidopsis T87 cultured cell under normal conditions
| PRJDB10546 | ENA
Project description:We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript.
2013-12-10 | GSE52468 | GEO
Project description:Genome-wide analysis of mRNA cleavage sites in Arabidopsis T87 cultured cell under heat stress condition
| PRJDB8951 | ENA
Project description:Comparison of Arabidopsis T87 cells transformed with an empty vector vs transcription factor (TF)-overexpressed lines of T87 cells.
2007-03-15 | E-ATMX-8 | biostudies-arrayexpress
Project description:We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript. Experiment using two-fractionated mRNA, Polysomal mRNA vs. total mRNA. Biological replicates: 1
2013-12-10 | E-GEOD-52468 | biostudies-arrayexpress
Project description:Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. Half-lives of average transcripts were determined to be elongated under cold conditions. Taking this general shift into account, we identified more than a thousand transcripts that were classified as relatively stabilized or relatively destabilized. The relatively stabilized class was predominantly observed in functional categories that included various regulators involved in transcriptional, post-transcriptional and post-translational processes. On the other hand, the relatively destabilized class was enriched in categories related to stress and hormonal response proteins, supporting the idea that rapid decay of mRNA is advanta- geous for swift responses to stress. In addition, pentatricopeptide repeat, cyclin-like F-box and Myb transcription factor protein families were significantly over-represented in the relatively destabilized class. The global analysis presented here demonstrates not only the importance of mRNA turn-over control in the cold stress response but also several structural characteristics that might be important in the control of mRNA stability. To demonstrate the importance of mRNA stability control in cold stress response, we investigated global changes in mRNA half-lives in response to cold treatment by micaroarray using Arabidopsis suspension cell cultures (T87 cells). Control cells were collected prior to transcriptional inhibitor (cordycepin) treatment (0 h), and 1 and 3 h after the start of cordycepin treatment. For cold-treated cells, 6 h samples were also used for microarray analyses. The experiments were performed with triplicate sets for each time point.
2012-12-16 | E-GEOD-31837 | biostudies-arrayexpress
Project description:We provide evidence that 5-EU metabolic labeling of Arabidopsis RNAs can be used for pulse-chase experiments, which allowed us to determine Arabidopsis RNA half-lives genome-wide without chemical inhibition of transcription. Similar to BRIC-Seq, we performed 5-EU IP chase (ERIC)-Seq in seedlings of A. thaliana. Hierarchical clustering of gene expression values allowed us to define at least five clusters of mRNAs that exhibited distinct degradation kinetics. To determine the RNA half-lives of each group, we applied an exponential decay model and a locally weighted scatterplot smoothing (LOWESS) and calculated the time where the concentration was halved. It became obvious that the half-lives determined by ERIC-Seq are much shorter than the ones determined after treatment with cordycepin or actinomycin D, respectively. We found that genes belonging to cluster A exhibiting the shortest half-lives are enriched in genes transcribed into non-coding RNAs, stress-related genes, genes involved in hormonal pathways and the metabolism of polyamines, which are also involved in stress responses. On the contrary, genes from cluster E, which have the longest half-lives, are specifically enriched in genes responsible for mitochondrial and plastic functions as well as primary metabolism (such as the TCA cycle)
2018-10-31 | GSE118461 | GEO
Project description:Genome-wide analysis of transcription start sites and mRNA translation state in Arabidopsis cells
| PRJDB3455 | ENA