GEO DataSets

(Submitter supplied) Identification of open chromatin in wheat spikes and seedlings using MH-seq

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

2 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome divergent regulation in the context of cellular differentiation. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

2 Samples

Download data: MTX, TSV

(Submitter supplied) Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

6 Samples

Download data: TXT

(Submitter supplied) Cuticular waxes coating leaf surfaces can help tolerate drought events by reducing non-stomatal water loss. Despite their role in drought tolerance, little is known about the cuticular wax responses of Canadian bread wheat varieties. To fill in this gap, RNAseq was performed on the flag leaf of four modern varieties to identify potential markers that could be used for selection of higher accumulation of cuticular waxes. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

12 Samples

Download data: XLSX

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

Organism:

Triticum aestivum

Type:

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

Platform:

GPL25409

46 Samples

Download data: BED, BW, TXT

(Submitter supplied) Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

12 Samples

Download data: TXT

(Submitter supplied) Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. more...

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

20 Samples

Download data: BW, TXT

(Submitter supplied) Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. more...

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

14 Samples

Download data: BED, BW

(Submitter supplied) Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. more...

Organism:

Triticum aestivum

Type:

Other

Platform:

GPL25409

1 Sample

Download data: TXT

(Submitter supplied) Here, we performed the cleavage under targets and tagmentation (CUT&Tag) assay, a recently developed technology for protein-DNA interaction, in protoplasts extracted from wheat root tissues to genome-widely identity the potential targets of TaSPL6-D. Using CUT-Tag-seq, we obtained 7,403 confidential peaks from two biological replicates, with which 2688 genes was associated. Zooming in the promoter region, GTAC motif was significantly enriched in the peaks. more...

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25409

3 Samples

Download data: NARROWPEAK

(Submitter supplied) We demonstrate here that heat stress severely alters the cytoskeletal configuration, cell structure, and global gene expression in male meiocytes and the tapetum layer, in a genotype-dependent manner. ‘Ellvis’, a heat-tolerant winter wheat cultivar, showed high fertility and only scarce structural aberrations upon exposure to high temperature. In addition, heat shock genes and genes involved in the alleviation of reactive oxygen species were significantly upregulated in ‘Ellvis’ and the expression of meiosis-specific and important developmental genes showed high stability in this cultivar. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

12 Samples

Download data: TXT

(Submitter supplied) Within a spike of wheat, the central spikelets usually generate three to four fertile florets, while the basal spikelets hardly achieve this. The physiological and transcriptional mechanism behind the difference in fertility between the basal and central spikelets is unclear. This study reports a high temporal-resolution investigation of transcriptomes, number and morphology of floret primordia, and physiological traits. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

34 Samples

Download data: TXT

(Submitter supplied) Climate change is not only causing a rise of global temperature but also more variable climates. In major wheat-producing countries, spring temperatures have increased up to 40°C in recent years. Considering the wheat optimal growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. To combat this threat, it is imperative to understand the response of wheat to early heat stress. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

30 Samples

Download data: TXT

(Submitter supplied) High plasticity of common wheat is attributed to the captured and polyploidization-promoted diversity. However, uncontrolled subgenome diversification can lead to hybrid conflict and dysgenesis, resulting in decreased diversity. How genomic diversity is maintained and interpreted to increase plasticity is unclear. By data-mining from the binding of 193 genome-wide trans-factors and genetic perturbations in common wheat, we identified LHP1 as a major regulator of subgenome-diversified defense genes, enhancer RNAs, and metabolite synthesis-related gene clusters via H3K27me3. more...

Organism:

Triticum aestivum

Type:

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

Platform:

GPL25409

21 Samples

Download data: BW, TXT, XLS

(Submitter supplied) Transcription start site (TSS) is the hub integrating regulatory input from promoters and enhancers. Common wheat converged three subgenomes adapted to different environment and established as a major crop worldwide. Detection of more precise and new TSS of both genes and enhancers in common wheat is the basis in interpreting transcriptional regulatory networks as well as the subgenome divergent regulation in their entirety.

Organism:

Triticum aestivum; Triticum urartu

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing

4 related Platforms

56 Samples

Download data: BED, BW, TXT

(Submitter supplied) To investigate how progressive drought stress affected gene expression during seed development

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

83 Samples

Download data: TAR

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

Organism:

Aegilops speltoides; Amblyopyrum muticum; Triticum dicoccoides; Aegilops bicornis; Aegilops searsii; Aegilops longissima; Triticum aestivum; Aegilops sharonensis

Type:

Expression profiling by high throughput sequencing; Other

8 related Platforms

122 Samples

Download data: TXT, VCF

(Submitter supplied) To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.

Organism:

Triticum aestivum; Aegilops speltoides

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25409 GPL31956

75 Samples

Download data: TXT

(Submitter supplied) A comparative RNA-Seq analysis was done in root and shoot of Najran wheat cultivar between plants grown under two conditions: control (0 mM NaCl) and salt treatment (200 mM NaCl). The current study revealed differentially expressed genes and various associated biological pathways involved in plant responses to salt stress between the two conditions in the root and shoot plant tissues, providing important insights into the molecular mechanisms underlying salt tolerance in wheat.

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

12 Samples

Download data: TXT

(Submitter supplied) More than four billion people rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. However, the changing climate threatens wheat production, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25409

28 Samples

Download data: TXT