GEO DataSets

(Submitter supplied) Purpose: Increasing biomass yield and quality of feedstock have been a recent interest in switchgrass research. Despite the economic importance of switchgrass, increasing temperature and water deficit are limiting factors to the cultivation of bioenergy crops in the semi-arid areas. The effect of individual drought or heat stress has been studied separately in switchgrass. However, there is relatively limited or no report on the molecular basis of combined abiotic stress tolerance in switchgrass particularly the combination of drought and heat stress. more...

Organism:

Panicum virgatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24761

54 Samples

Download data: TSV

(Submitter supplied) The combined heat and drought stress influence the plant growth and development. Switchgrass is an economically important crop due to the availability of high biomass with little water and nutrient requirements. Earlier reports suggested that switchgrass growth and yield highly influenced by heat and drought. The mechanism behind heat and drought stress is not fully understood in switchgrass. This study has undertaken to analyze the epigenetic modification using ChIP-Seq analysis with the activation histone mark H3K4me3. more...

Organism:

Panicum virgatum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31915

63 Samples

Download data: BW

(Submitter supplied) Purpose: Brassica. juncea is vulnerable to abiotic stresses at specific stages in its life cycle. However, till date no attempts have been made to elucidate the genome-wide changes in the transcriptome of B. juncea subjected to either high temperature or drought stress. Hence, to gain global insights into genes, transcription factors and kinases regulated by these stresses and to provide basic information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de novo assembly to discover B. more...

Organism:

Brassica juncea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16439

6 Samples

Download data: BED, DIFF, FA, FPKM_TRACKING, TXT

(Submitter supplied) In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. more...

Organism:

Panicum virgatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18719

119 Samples

Download data: TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9062 GPL198

12 Samples

Download data: CEL, TAR, XLS

(Submitter supplied) These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Keywords: stress response, histone modification

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: TAR, XLS

(Submitter supplied) These microarrays are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels (via ChIP-seq) in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Water deficit stress causes a large number of genes to change their transcript levels, which provided a large set of genes to examine for corresponding chromatine changes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

16 Samples

Download data: TXT

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT

(Submitter supplied) Sorghum is an important crop often subjected to simultaneous high temperatures and drought in the field. We examined the gene expression response to heat and drought stress both individually, and in combination, with the aim of identifying important stress tolerance mechanisms.

Organism:

Sorghum bicolor

Type:

Expression profiling by array

Platform:

GPL17335

12 Samples

Download data: TXT

(Submitter supplied) Durum wheat is an important cereal crop grown mainly in semi-arid environments (e.g. Mediterranean regions) characterized by water scarcity and high temperatures often occurring at the same time. This work reports on a transcriptomic analysis carried out on two durum wheat cultivars (Cappelli and Ofanto) characterized by different water use efficiency (WUE), grown to booting stage and subjected to a combination of drought and heat stresses, a situation similar to the experience of a crop grown in Mediterranean environments and exposed to a terminal heat/drought stress. more...

Organism:

Triticum aestivum; Triticum turgidum subsp. durum

Type:

Expression profiling by array

Platform:

GPL3802

24 Samples

Download data: CEL

(Submitter supplied) Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. more...

Organism:

Triticum turgidum subsp. durum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL28728 GPL20257

136 Samples

Download data: XLSX

(Submitter supplied) To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: TXT

(Submitter supplied) The moss Physcomitrella patens was employed to study abiotic stress responses in order to understand the effects of mild (30°C) and strong (37°C) continuous heat stresses from 1h to 24h at a transcriptomic level.

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17793

24 Samples

Download data: TXT

(Submitter supplied) To investigate changes in genome methylation in flax seedlings under drought stress, we selected a drought-tolerant flax variety (Z141) and a drought-sensitive flax variety (NY-17) We then performed genome methylation analysis using data obtained from Z141 and NY-17 leaf tissue BS-seq at four different treatments (DS, RW, RD and CK).

Organism:

Linum usitatissimum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL32467

24 Samples

Download data: BEDGRAPH

(Submitter supplied) Heat stress is a major limiting factor for grain yield and grain quality in wheat production. In crops, abiotic stresses have transgenerational effects and the mechanistic basis of stress memory is associated with epigenetic regulation. The current study presents the first systematic analysis of the transgenerational effects of post-anthesis heat stress in tetraploid wheat. Genotype-dependent response patterns to parental and progeny heat stress were found for the leaf physiological traits, harvest components, and grain quality traits measured. more...

Organism:

Triticum turgidum subsp. durum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL20257 GPL28728

24 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20705

32 Samples

Download data

(Submitter supplied) Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20705

12 Samples

Download data: FPKM_TRACKING, GTF