GEO DataSets

(Submitter supplied) Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in hdp1-1 and hdp2-1 mutants

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(Submitter supplied) Purpose:Comparative transcriptome analyses was applied to characterize gene expression after overexpression GaTOP6B in Arabidopsis thaliana. Methods:The fresh leaves were collected from 4-week-old WT plants and transgenic Arabidopsis lines under drought treatments. The total RNA was first extracted using TRIzol Reagent (TaKaRa, Tokyo, Japan), and treated with RNase-free DNase I (TaKaRa), and then followed with mRNA purification using the Magnetic Oligo (dT) Beads (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: XLSX

(Submitter supplied) We observed that the Arabidopsis endo-1,4-mannanase gene AtMAN6 is involved in the formation of cell walls in vascular tissues. In the inflorescence stem, the man6 mutant had smaller vessel cells with thicker secondary cell walls and shorter fiber cells. Elongation growth was reduced in the root, and secondary cell wall deposition in vessel cells occurred early. Overexpression of AtMAN6 resulted in the inverse phenotypes of the man6 mutant. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

5 Samples

Download data: XLSX

(Submitter supplied) Next-generation sequencing (NGS) has been used to study the differential gene expression in Arabidopsis green seedlings under warm temperature. The goal of this study is to investigate how ethylene signaling and epigenetic modification are involved in transcriptional regulation in response to warm temperature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

20 Samples

Download data: CSV, TXT

(Submitter supplied) Abscission is a developmental process that sheds organs in response to developmental and environmental cues. Abscission involves cell separation between two neighboring cell types in the abscission zone (AZ), residuum cells (RECs) and secession cells (SECs). However, the regulatory mechanisms for spatial determination governing cell separation are poorly understood. BREVIPEDICELLUS (BP) is one of the key transcription factors regulating the AZ cell size and number. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19580 GPL13222

108 Samples

Download data: TXT

(Submitter supplied) The hormone abscisic acid (ABA) regulates many plant stress responses and plant development by activating a complex gene regulatory network. This time series experiment was designed to unravel the architecture and dynamics of the ABA gene regulatory network.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

63 Samples

Download data

(Submitter supplied) The development of multi-cellular organisms requires coordinated changes in gene expression that are often mediated by the interaction between transcription factors (TFs) and their corresponding cis-regulatory elements (CREs). During development and differentiation, the accessibility of CREs is dynamically modulated by the epigenome. How the epigenome, CREs and TFs together exert control over cell fate commitment remains to be fully understood. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19580 GPL13222

5 Samples

Download data: BW

(Submitter supplied) The developmental functions of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) 10 have been extensively studied in Arabidopsis, but SPL10's role in regulating leaf curvature has not been well characterized. In this study, we observed an upward-curling leaf phenotype upon overexpression of a miR156/157-resistant version of SPL10 (rSPL10). DNA affinity purification sequencing (DAP-seq), RNA-seq, and transient transactivation assays revealed that SPL10 binds to the promoter of REVOLUTA (REV). more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL13222

3 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) The goal of this study is to clarify the function of LBD29 and MYB2 in the pathway of lateral root development. We isolated total RNA from the roots of 8-day-old Col-0 and sevaral transgene seedlings. New genes act downstream of LBD29 and MYB2, during the lateral root formation, are discovered.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: CSV

(Submitter supplied) Purpose: To understand the molecular mechanism between PNET2 and NTLs, we generated 35S:NTL-SRDX in pnet2_ab mutants to suppress NTL gene expression and performed the whole genome transcriptome analysis on 4-week-old plants of WT, pnet2_ab, 35S:NTL6-SRDX pnet2_ab, 35S:NTL9-SRDX pnet2_ab, and 35S:NTL12-SRDX pnet2_ab. Conclusions: PNET2 regulates diverse responses by associating with a family of membrane-bound transcriptional factors.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

10 Samples

Download data: TXT

(Submitter supplied) To identify new regulators of stomatal development, we assay the transcriptomes of plants bearing enriched stomatal lineage cells undergoing active divisions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TXT, XLSX

(Submitter supplied) We conducted ChIP-seq technology to generate epigenomic profiles of H3K4me3, H3K27me3 and H3K9me2 in Arabidopsis leaves for the mutant (kaku4-2) and wild-type (WT) plants. The results showed that knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least effect on H3K4me3, leading to significant change of chromatin states in Arabidopsis genome. KAKU4 may affect the switch between active and repressive chromatin states, especially knockdown of KAKU4 caused the transition between H3K9me2 and H3K27me3 in some specific PLAD regions. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL13222 GPL26208

12 Samples

Download data: BW, TXT

(Submitter supplied) The intricate interactions between plants and microorganisms have garnered substantial scientific interest. While previous studies have highlighted the potential influence of various fungal volatile compounds(VCs) on plant growth and development, the precise mechanisms underlying this modulation still need to be discovered. In this study, we discovered that fungal volatile organic compounds from the soil-borne fungus Tolypocladium inflatum GT22 enhance the growth of Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) We conducted the combination analysis of transcriptomic and epigenomic data between kaku4-2 mutant and WT suggested that KAKU4 may inhibit the expression of a series of genes related to hormone signals and H2O2 metabolism by affecting the deposition of H3K27me3, thereby suppressing leaf senescence.

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL26208 GPL13222

8 Samples

Download data: BW, TXT

(Submitter supplied) RNA-sequencing was performed using Col-0 and hfr1-4pil1-2 seedlings upon 96 hours (96hr) low R:FR treatment. We analysed global gene expression changes in Arabidopsis thaliana in response to 96hr low R:FR, in order to identify the different effects of negative regulator in long-term treatments.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) Absence of miRNA in dcl1 mutant activates global translation-independent 5’->3’ exonucleolytic decay to maintain robust mRNA abundance of miRNA target genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL13222 GPL24270

16 Samples

Download data: BW, TXT

(Submitter supplied) Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT