Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1262915 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33561000_1.fastq.gz | Fastqsanger.gz | |||
| SRR33561000_2.fastq.gz | Fastqsanger.gz | |||
| SRR33561001_1.fastq.gz | Fastqsanger.gz | |||
| SRR33561001_2.fastq.gz | Fastqsanger.gz | |||
| SRR33561002_1.fastq.gz | Fastqsanger.gz |
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Project description:To understand affected genes by overexpression of origouridylate binding protein 1b (UBP1b) under heat stress conditions, transcriptional profiling of UBP1box and control plants were analyzed under normal and heat stress (40°C) conditions using Arabidopsis custom microarrays.
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Project description:To understand affected genes by overexpression of origouridylate binding protein 1b (UBP1b) under heat stress conditions, transcriptional profiling of UBP1box and control plants were analyzed under normal and heat stress (40°C) conditions using Arabidopsis custom microarrays. Microarray analysis was conducted using UBP1b-ox and Venus control plants subjected to non-stress and heat-stress condition for 1 h.
2016-08-21 | E-GEOD-78713 | biostudies-arrayexpress
Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress.
2010-04-23 | GSE17514 | GEO
Project description:Elevated temperature occurring at reproductive stage has great impact on gametophyte development and therefore ultimate fruit or seed set in plants, the underlying molecular mechanisms are less understood. We investigated the effect of elevated temperature stress on reproductive development in Arabidopsis with tissue-specific transcriptome profiling and observed distinct response patterns between vegetative and reproductive tissues. Heat stress exposure affected reproductive developmental programs including early phases of anther/ovule development and meiosis process, and genes participating in the unfolded protein response (UPR) were enriched among the heat up-regulated reproductive tissue-specific genes. We found that the bzip28bzip60 double mutant defective in UPR were sensitive to elevated temperature stress in terms of reduced silique length and fertility comparing to the wild-type plants. Comparison of heat responsiveness between the wild-type and bzip28zip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress at reproductive stage, most of which were non-canonical UPR genes. Further ChIP-Seq data revealed 133 direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, of which 39 target genes were up-regulated by heat stress at reproductive stage. Our results provide novel insights into heat responsiveness in reproductive tissues and demonstrate the protective roles of UPR for maintaining fertility upon heat stress in plants.
2017-03-15 | GSE94146 | GEO
Project description:Purpose: To understand time of day variation in Arabidopsis heat shock responses. We have observed significant differences in terms of plant survivability in response to a heat shock across various times of day. Because of this, we believe that transcriptional responses may be a significant underlying factor which contributes to the observed physiology and surivability after heat stress. Methods: Whole plant tissue mRNA profiles in Col-0 Arabidopsis were generated by deep sequencing using Illumina HiSeq 2500. Tissue samples of four replicates were collected at two times of day (Dawn and Dusk, ZT0/ZT12) and were either control or heat stressed (30oC) for 1 hour. An additional 4 samples were collected in constant light conditions (single replicate) to quantify circadian effects. Sequence reads from each sample were mapped to the TAIR10 reference genome with Tophat2 and counts were obtained using Htseq-count. Differential expression analysis was done using DeSeq2 to calculate differential expression levels of each gene in the dataset. Results: We identified 5512 differentially expressed transcripts with our DESeq2 based data analysis pipeline that involves characterizing gene expression profiles based on basal expression level, time of differential expression, and direction of differential expression. An additional interaction term analysis revealed 572 genes which showe time of day dependent responses to heat stress, meaning the response to heat stress differs depending on the time of day that the heat stress is perceived by the plant. Downstream analysis using gene ontology analysis tools (Pantherdb.org) and Cytoscape revealed strong differences in terms of response happening in the AM and PM gene expression networks. The significance of this work is that it is the first study to show that there is a significant difference in terms of transcriptional responses to heat stress in Arabidopsis where the differences were quantified by levels of mRNA expression.
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Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species. Analysis of genetic element transcriptional changes in response to 6 hours of 37°C heat stress and 48 hours of recovery in Arabidopsis thaliana Col-0 and Arabidopsis lyrata MN47.
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Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress. Three independent 200 ml cultures of wild-type and rpd3Δ mutant strains were grown to mid-log phase in YPD rich medium at 25ºC (control) or at 39 ºC for 20 min (heat stressed). Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.
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