GEO DataSets

(Submitter supplied) A period of exposure to high ambient temperatures can damage the process of grain filling in rice, potentially inducing the endosperm to become chalky. Given the established involvement of long non-coding RNAs (lncRNAs) in regulating plant development and its stress response, the purpose here was to reveal the extent to which lncRNA activity contributes to the endosperm chalkiness syndrome. Among 578 lncRNAs identified in spikelets harvested ten days post anthesis from plants exposed to high temperature stress, 14 were found to be more abundant than in control plants, while 45 were less abundant. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL21812

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The environment plays important role in the interaction between plant hosts and pathogens. The application of chemical fertilizer is a crucial breeding technology to enhance crop yield since last century. As the most abundant fertilizer, nitrogen often increases disease susceptibility for crop plants. The underlying mechanism for nitrogen induced disease susceptibility is elusive. Here we found that nitrogen application activate gibberellin signaling by degradation of SLR1, the repressor protein in gibberellin signaling, which result in simultaneously promoting plant growth and disease susceptibility. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

12 Samples

Download data: TDF

(Submitter supplied) Rice (Oryza sativa) is one of the world's major rations. The widely planted hybrid rice in Jiangxi Province is seriously affected by Magnaporthe oryzae, which seriously restricts the rice yield in Jiangxi Province. In recent years, studies have found that alternative polyadenylation (APA) is an important post-transcriptional regulation in eukaryotes. The genetic law and function of APA in the occurrence of hybrid rice blast in Jiangxi are not clear. more...

Organism:

Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27860 GPL31130

75 Samples

Download data: TXT

(Submitter supplied) Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Although hundreds of stress-related genes have been identified in the past two decades, very few genes have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, identified through NAC-centered gene regulatory network and genetic association analyses, is a hub stress-regulator that integrates the regulations of both drought and heat tolerance in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL23876

49 Samples

Download data: BW, TXT

(Submitter supplied) Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27860

32 Samples

Download data: TSV, TXT

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13834 GPL27860

75 Samples

Download data: BIGWIG, BW, COV

(Submitter supplied) To investigate the effect of the OsINO80, we analysed differentially expressed genes of osino80 mutant compared to WT. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and osino80 mutant.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

6 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27860 GPL13834

61 Samples

Download data: BIGWIG

(Submitter supplied) To investigate the effect of the OsINO80, we analysed DNA methylation of osino80 mutant compared to WT.

Organism:

Oryza sativa Japonica Group

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27860

8 Samples

Download data: COV

(Submitter supplied) Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

9 Samples

Download data: TXT

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL27860

21 Samples

Download data

(Submitter supplied) I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences, which can be formed under various pH conditions. DNA methylation exhibits complex impacts on iM formation in vitro. However, how DNA methylation differentially affects pH dependent iM formation on a genome wide scale is completely uncharacterized in both humans and plants. To this end, we conducted iM-IP-seq under pH 5.5 and 7.0 conditions using CK and hyper/hypomethylated DNA in combination with BS-seq in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27860

17 Samples

Download data: NARROWPEAK

(Submitter supplied) I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences, which can be formed under various pH conditions. DNA methylation exhibits complex impacts on iM formation in vitro. However, how DNA methylation differentially affects pH dependent iM formation on a genome wide scale is completely uncharacterized in both humans and plants. To this end, we conducted iM-IP-seq under pH 5.5 and 7.0 conditions using CK and hyper/hypomethylated DNA in combination with BS-seq in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27860

4 Samples

Download data: TXT

(Submitter supplied) Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

48 Samples

Download data

(Submitter supplied) Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

21 Samples

Download data: XLS

(Submitter supplied) Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

27 Samples

Download data: XLS

(Submitter supplied) Purpose: The goals of this study are screening the putative target genes regulated by OsNF-YA5 using DEX(dexamethason) inducible system. Methods: 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media were treated with 50 μM dexamethasone (DEX) solution containing 0.02% (w/v) Silwet L-77. For mock treatments, 0.02% Silwet L-77 was sprayed into rice plants. To minimize the effect by the treatment, plants were pre-treated with 0.02% Silwet L-77 3 hours before DEX treatment). more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

8 Samples

Download data: GTF, TXT

(Submitter supplied) we monitored the responsive changes of rice genes at 0 and 6 hours across Xoo pathotype GIV infection in Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor by RNA sequencing. These findings provide new insights for directly identifying iTALEs-targeted resistance gene and the regulatory roles of OsTOPBP1C in rice-Xoo interactions.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

18 Samples

Download data: TXT

(Submitter supplied) Eukaryotes gene expression of mRNA and protein is a basic cellular activity and regulated by multiple process, yet the expression patterns at these two levels and their genetic and evolutionary determinants remain undefined in plants. Here, using RNA-sequencing and TMT labeled LC-MS/MS analysis, we investigated the genome-wide variation of mRNA and protein expression in rice subspecies japonica C92, indica MH63 and their F1 hybrid. more...

Organism:

Oryza sativa Indica Group; Oryza sativa Japonica Group; Oryza sativa Indica Group x Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27960 GPL21027 GPL18525

9 Samples

Download data: TXT

(Submitter supplied) We investigated the function of the plant-specific SR protein SC106 in pre-mRNA splicing regulation and abiotic stress responses in rice. The loss-of-function mutant, SC106, showed increased sensitivity to salt. We performed genome-wide analyses of gene expression and splicing in seedlings subjected to salt stress and identified multiple splice isoforms from stress-responsive genes dependent on SC106.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27860

12 Samples

Download data: XLSX