E-ENAD-8
Ontology highlight
ABSTRACT:
PROVIDER: E-ENAD-8 | ExpressionAtlas | 2018-01-04
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-ENAD-8-analysis-methods.tsv | Tabular | |||
| E-ENAD-8-analytics.tsv | Tabular | |||
| E-ENAD-8-atlasExperimentSummary.Rdata | Rdata | |||
| E-ENAD-8-configuration.xml | Xml | |||
| E-ENAD-8-g1_g2-mvaPlot.png | Other |
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Project description:The shoots and roots of a plant respond differently to osmotic stress, as they have distinct functions and anatomical structures. Under conditions of high solute concentration, such as in saline soils or drought, water uptake by the roots is reduced, resulting in cellular dehydration. In this study, we performed transcriptional profiling of roots of Arabidopsis under osmotic stress conditions such as high salinity and drought using mRNA-Seq for the assessment of gene expression changes in roots of Arabidopsis. mRNA-Seq analysis showed that many differentially expressed genes showed differential expressions under both salt stress and drought stress conditions in roots and were distinct from aerial parts. We confirmed 68 transcription factor genes which is involved in osmotic stress signal transduction in roots and are connected tightly. Interestingly, well-known ABA-dependent and/or -independent osmotic stress-responsive genes were less increased in roots, indicating that osmotic stress response in roots might be regulated by stress pathways other than well-known pathways. We identified 26 osmotic stress-responsive genes, which have alternative splicing variant isoforms, showed distinct expression in roots under osmotic stress conditions from the mRNA-Seq analysis. Quantitative RT-PCR confirmed that alternative splicing variants, such as ANNAT4, MAGL6, TRM19, and CAD9, have differential expressions in roots under osmotic stress conditions, indicating that alternative splicing is an important regulatory mechanism in osmotic stress response in roots. Taken together, our study suggest that many transcription factor families are involved in osmotic stress response in roots and tightly connected each other. In addition, alternative splicing and function of alternative splicing variant isoforms are also important in osmotic stress response in roots. To understand the alternative splicing mechanism in roots, further study is necessary.
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Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions. We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.
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Project description:In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT and µlox seedling roots and shoots under 30% PEG -induced osmotic shock and control conditions and after 0, 1, 2, 3 h.
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Project description:In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT and µlox seedling roots and shoots under 30% PEG -induced osmotic shock and control conditions and after 0, 1, 2, 3 h.
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