Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA278120 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1915004.fastq.gz | Fastqsanger.gz | |||
| SRR1915974.fastq.gz | Fastqsanger.gz | |||
| SRR1915975.fastq.gz | Fastqsanger.gz | |||
| SRR1915976.fastq.gz | Fastqsanger.gz |
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Project description:Micro RNAs (miRNAs) are a class of small endogenous RNAs conserved in eukaryotic organisms including plants. They suppress gene expression post-transcriptionally in many different biological processes. Previously, we reported salinity-induced changes in gene expression in transgenic Arabidopsis thaliana plants that constitutively expressed a pea abscisic acid-responsive (ABR17) gene. In the current study, we used a microarray to investigate the role of miRNA-mediated post-transcriptional gene regulation in these same transgenic plants in the presence and absence of salinity stress. We identified nine miRNAs that were significantly modulated due to ABR17 gene expression, and seven miRNAs that were modulated in response to salt stress. The target genes regulated by these miRNAs were identified using starBase (sRNA target Base) Degradome analysis and through 5' RNA Ligase Mediated-Rapid Amplification of cDNA Ends (RLM-RACE). Our findings revealed miRNA:mRNA interactions comprising regulatory networks of Auxin Response Factor (ARF), ARGONAUTE 1, (AGO1), Dicer-like proteins 1 (DCL1), Squamosa Promoter Binding (SPB), NAC, APETALA 2 (AP2), Nuclear Factor-Y (NFY), RNA binding proteins, Arabidopsis thaliana vacuolar phyrophosphate 1 (AVP1) and Pentatricopetide repeat (PPR) in ABR17 transgenic A. thaliana, which control physiological, biochemical and stress signalling cascades due to the imposition of salt stress. Our results are discussed within the context of the effect of the transgene, ABR17, and the roles miRNA expression may play in mediating plant responses to salinity.
2014-01-31 | GSE53783 | GEO
Project description:Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distribute in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that this highly conserved modification was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: 3810 normalized 2-hydroxyisobutyrylation sites on 1254 proteins were identified in siliques under salt stress, and lysine 2-hydroxyisobutyrylation was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants.
2021-12-30 | PXD026643 | Pride
Project description:Arabidopsis thaliana Transcriptome under Salt Stress
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Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:CuZn-superoxide dismutase (CuZn-SOD) and ascorbate peroxidase (APX) constitute first line of defence against oxidative stress. In the present study, PaSOD and RaAPX genes from Potentilla atrosanguinea and Rheum australe, respectively were overexpressed individually as well as in combination in Arabidopsis thaliana. We performed RNA-seq analysis of wild type and transgenic Arabidopsis thaliana overexpressing CuZn-SOD, APX and CuZn-SOD + APX under control and salt stress
2014-10-06 | E-MTAB-4434 | biostudies-arrayexpress
Project description:High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. Transcriptomic and proteomic analyses of the salt-treated sahy9/apum23 and wild-type seedlings revealed differential expression of genes with similar functional categories, primarily including cellular and metabolic processes, and abiotic and biotic stress responses. However, the consistency of gene expression at both transcript and protein levels is low (), suggesting the involvement of posttranscriptional processing in salt response. Furthermore, the altered gene/protein expression mediated by SAHY9/APUM23 in salt sensitivity is involved in several functional groups, particularly in ABA biosynthesis and signaling, abiotic stress response, LEA proteins, and ribosome biogenesis-related genes. Importantly, NCED3, a key gene involved in ABA biosynthesis, and major ABA responsive marker genes, such as RD20 and RD29B, are down-regulated at both transcript and protein levels in sahy9/apum23 under salt stress. Consistently, lower contents of ABA and proline, and expression changes of a subset of LEA proteins also support the nature of sahy9/apum23 showing salt hypersensitivity. Collectively, these data suggest that SAHY9/APUM23-mediated salt response is associated with ABA signaling pathway and its downstream stress responsive or tolerant genes.
2018-02-20 | GSE99664 | GEO
Project description:Salt stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a novel calcium-binding protein and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rsa1-1 mutation on global gene expression in response to 120 mM Nacl for 0 or 24 h. A set of genes differentially expressed in rsa1-1 with or without salt stress are identified. Six-day-old seedlings of Arabidopsis thaliana wild type (Columbia gl1 expressing RD29A::LUC transgene) and rsa1-1 mutant seedlings subjected to salt stress with 120 mM NaCl for 0, or 24 h were used for total RNA extraction and hybridizations with Affymetrix ATH1 GeneChips. There are three biological replicate per genotype.
2013-07-07 | E-GEOD-39236 | biostudies-arrayexpress
Project description:Arabidopsis thaliana is a glycophyte with a low salt tolerance, while Eutrema is a halophyte with a very high salt tolerance. To elucidate the transcriptional basis of this difference, we performed hydroponis culture experiments where we grew plants under control conditions (25 mM NaCl) or under salt stress (200 mM NaCl for both species, 500 mM for Eutrema). Salt concentration was increased for the stress treatments by increments of 50 mM per day (25 mM on the first day). Plants were grown at the final NaCl concentration for an additional week, when rosettes were harvested for RNA isolation.Expression patterns were compared between treatments and between species.
2016-06-29 | GSE71271 | GEO
Project description:Transcriptional profiling of Arabidopsis thaliana cotyledons comparing ecotype Col-0 (Control) with lea13 T-DNA line to elucidate the response mechanism to drought stress conditions that rely on LEA protein function.
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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
2013-01-31 | E-GEOD-41935 | biostudies-arrayexpress