E-CURD-1
Ontology highlight
ABSTRACT:
PROVIDER: E-CURD-1 | ExpressionAtlas | 2019-10-04
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-CURD-1-analysis-methods.tsv | Tabular | |||
| E-CURD-1-atlasExperimentSummary.Rdata | Rdata | |||
| E-CURD-1-coexpressions.tsv.gz | Tabular | |||
| E-CURD-1-configuration.xml | Xml | |||
| E-CURD-1-factors.xml | Xml |
Items per page: 5 1 - 5 of 187 |
Similar Datasets
Project description:Purpose: In this study we investigated the role of JASMONATE RESISTANT 1 (JAR1) and JAR1 mediated JA-Ile formation in drought stress tolerance in Arabidopsis thaliana. Methods: Global transcriptional changes in a newly generated over-expression line (JAR1-OE; 35S::JAR1-1-YFP)), a T-DNA insertion line in the JAR1 locus (jar1-11;SALK_034543), and wild-type Col-0 were investigated by RNA-seq analyses of rosette leaves from 32 day-old plant that were either well-watered (control) or not watered after day 18 (drought). Plants were grown on soil under long-day conditions Results: Under control conditions, using a stringent cut-off (DESeq, adjusted to FDR < 0.01 and LogFC ≥ 1), we found only four differentially expressed genes (DEGs) between jar1-11 and Col-0, all of them downregulated. By contrast, we found 339 DEGs between JAR1-OE and Col-0, of which 134 were downregulated and 205 were upregulated. A comparison of the RNA-seq data from Col-0 between control and drought conditions revealed 3401 DEGs, of which 2023 were down- and 1378 upregulated. By comparison, jar1-11 plants, which were most heavily affected by drought stress, showed a much higher number (6139 in total; 2616 up- and 3523 down-regulated) of DEGs, while the more drought-tolerant JAR1-OE line displayed a lower number (2025 in total; 971 up- and 1054 down-regulated) of DEGs. 2411 DEGs were found between Col-0 and jar1-11 under drought among which 966 genes showed a higher and 1445 genes a lower expression level in jar1-11. On the other hand, out of 998 DEGs found between Col-0 and JAR1-OE under drought, 737 genes showed a higher and 261 genes a lower expression level in JAR1-OE. Moreover, we found 391 DEGs counter-regulated between jar1-11 and JAR1-OE. Conclusion:RNA-seq analysis and additional experiments of plants under control and drought stress conditions provided insight into the molecular reprogramming caused by the alteration in JA-Ile content.
2022-07-25 | GSE196602 | GEO
Project description:Arabidopsis thaliana Col-0 plants were compared to sir1-1 T-DNA insertion mutants to investigate transcript levels of sulfur metabolism related genes under standard conditions.
2010-03-12 | GSE20670 | GEO
Project description:Background: Skewing root patterns provide key insights into root growth strategies and mechanism that produce root architectures Roots exhibit skewing and waving when grown on a tilted, impenetrable surface, and while the genetics guiding these morphologies have been examined, the underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing. WS is a skewing ecotype. Col-0 is a non-skewing ecotype. Results: This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling. Conclusions: Many of the 11 identified genes are involved in signaling and perception, rather than the physical restructuring of roots, leading to the conclusion that root skewing is enabled through diverse environmental signaling pathways. These findings revealed further insights into the molecular mechanisms behind root skewing. This work investigated the transcriptional differences between skewing and non-skewing roots. Comparisons within WS revealed gees that that responded to the angle of growth (Agp) during the process of skewing. These genes were cross referenced with transcripts differing between the WS and Col-0 genotypes to refine the list of genes that are most probably be involved in root skewing. More of the highly probable skew gene candidates (HPSGC) are associated with environmental sensing (e.g. salt, sugar, hormones, darkness) than with physical growth differences (e.g. cell wall remodeling, cell division, cell elongation). Thus, the root behavior of skewing appears to be primarily driven by pathways that respond to disparate signals from the root local environment. Future studies could investigate the HPSGC to find the specific pathways and molecular mechanisms contributing to root skewing.
2016-08-31 | GSE83242 | GEO
Project description:Transcriptional comparison of Arabidopsis thaliana pvip1;pvip2 RNAi double mutants against Col-0 wildtype. Tissue used: whole rosettes of 4-week-old plants grown under short-day conditions (8h light; 20oC). 3 biological replicates for each. Control = Col-0 and mutant = pvip1;pvip2. PVIP = Potyvirus-VPg-interacting protein (Dunoyer et al. 2004 J. Virol. 78: 2301-2309).
2009-12-11 | GSE19341 | GEO
Project description:To understand affected genes by HDA19 and HDA5/14/15/18 under salinity stress conditions, hda19 and hda5/14/15/18 mutants and control (Col-0) plants were analyzed under normal and salinity stress conditions using Arabidopsis custom microarrays (GEO array platform: GPL19830).
2017-10-15 | GSE90562 | GEO
Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison
2014-11-02 | GSE59556 | GEO
Project description:The aim of this study was to perform a transcriptional characterization of the Arabidopsis eds4 mutant. To this end two separate experiments were performed: Experiment 1: comparison of the transcriptional profile (RNA-seq) of eds4 Arabidopsis mutants in contrast to wild type Col-0 accession grown under continuous light conditions. Experiment 2: Analysis of the distribution of transcripts (RNA-seq) between nucleus and cytoplasm in the eds4 Arabidopsis mutants in comparison to wild type Col-0 plants grown under continuous light conditions.
2020-01-01 | GSE120757 | GEO
Project description:Phosphate limitation constrains plant development in natural and agricultural systems. Under phosphate-limiting conditions plants activate genetic, biochemical and morphological modifications to cope with phosphate starvation. One of the morphological modifications that plants induce under phosphate limitation is the arrest of primary root growth and it is induced by the root tip contact with low phosphate media. The sensitive to proton rhizotoxicity (stop1) and aluminium activate malate transporter 1 (almt1) mutants of Arabidopsis thaliana continue primary root growth under in vitro Pi-limiting conditions, thus, to get insight into the molecular components that control primary root growth inhibition under low phosphate conditions we extracted and sequenced mRNA from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and low-phosphate-insensitive mutants almt1 and stop1 grown under low and high phosphate conditions 5 days after germination using an RNA-seq methodology.
2017-08-22 | GSE90061 | GEO
Project description:To understand the effect of HDA19 deficiency in hda5/14/15/18 (quad) under salinity stress conditions, hda19, quad, hda5/14/15/18/19 (quint) mutants and control (Col-0) plants were analyzed under normal and salinity stress conditions using Arabidopsis custom microarrays (GEO array platform: GPL22706).
2019-09-10 | GSE121225 | GEO
Project description:Purpose: The aim of this study is to investigate the role of H3K9 methylation in the development of syncytia induced by the beet cyst nematode (BCN, Heterodera schachtii). For this, differential gene expression analysis was performed in root tissues of Col-0 wild-type and suvh5 and suvh6 single mutants under BCN-infected and noninfected conditions. Methods: Col-0 wild-type and suvh5 and suvh6 mutant plants were grown and 10-day-old plants were inoculated with 100 second-stage juvenile (J2) H. schachtii at 10 days old. Five days post inoculation, root tissues were collected from infected and noninfected plants in triplicate. Total RNA was extracted, mRNA libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovoSeq 6000. High quality, paired-end reads were then aligned to the Arabidopsis thaliana reference genome (TAIR10.28) using STAR and uniquely mapped reads were counted using HTSeq. Finally, differentially expressed genes (DEGs) between the mutant lines and wild-type plants under non-infected and infected conditions were identified using DESeq package. Results and conclusions: At least 20 million reads were uniquely mapped to the Arabidopsis reference genome with an average length of about 300 bp for paired-end reads. A total of 1057 and 3390 DEGs were identified for suvh5 and suvh6 versus Col-0, respectively, under noninfected conditions. Upon infection of BCN, Col-0 had 4566 DEGs compared to the noninfected wild type. BCN-infected single mutants suvh5 and suvh6 had 2487 and 846 DEGs compared to BCN-infected Col-0, respectively. Of these DEGs, 1277 and 592 or about 51% and 70% are also differentially expressed in BCN-infected Col compared to noninfected Col-0, respectively, and 324 of the 1277 and 592 DEGs are common to BCN-infected suvh5 and suvh6 compared to the control. DEGs common to BCN-infected Col-0 and/or suvh5, and suvh6 are involved in stress and defense responses, primary and secondary metabolism, signal transduction, cell wall organization and other cellular processes. This suggests that SUVH5 and SUVH6 play a major role in transcriptome reprogramming to facilitate cellular, molecular, and metabolic processes involved in the compatible plant-nematode interaction.
2022-05-03 | GSE173818 | GEO