GEO DataSets

(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) The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. more...

Organism:

Triticum urartu

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29754

2 Samples

Download data: BW, XLS

(Submitter supplied) The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. more...

Organism:

Triticum urartu

Type:

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

Platforms:

GPL29755 GPL29754

25 Samples

Download data: BW, TXT

(Submitter supplied) The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. more...

Organism:

Triticum urartu

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29754

119 Samples

Download data: BW, TXT

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

Organism:

Triticum urartu

Type:

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

Platforms:

GPL29754 GPL29755

146 Samples

Download data: BW, TXT, XLS

(Submitter supplied) Endosperms (with the embryo, aleurone, seed coat, and pericarp removed) at 5, 10, 15, 20, and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated and a library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA). An integrated reference sequence of T. more...

Organism:

Triticum urartu

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23449

18 Samples

Download data: XLSX

(Submitter supplied) In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that retrotransposon-derived back-spliced RNA can bind to the centromere through R-loops and regulate the formation of centromeric chromatin loops. Multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and back spliced RNA from CRM1 were detected. more...

Organism:

Triticum urartu; Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27486 GPL17628

3 Samples

Download data: TXT

(Submitter supplied) Polyploidy occurs in some animals and all flowering plants including important crops such as wheat. The consequences of polyploidy on crops remain elusive partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids SSAA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. more...

Organism:

Aegilops tauschii; Aegilops longissima; Aegilops longissima x Triticum urartu; Triticum urartu; Triticum urartu x Aegilops tauschii

Type:

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

5 related Platforms

45 Samples

Download data: FASTA, FPKM_TRACKING, GTF, TXT

(Submitter supplied) To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized

Organism:

Triticum aestivum; Triticum urartu; Aegilops speltoides; Aegilops tauschii; Secale cereale

Type:

Expression profiling by array

Platform:

GPL18847

12 Samples

Download data: PAIR, TXT