GEO DataSets

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21027 GPL27960 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

(Submitter supplied) Cold is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in plants. R-loops can function in a series of biological processes, including normal development and stress responses, in plants. However, how R-loops function in cold responses is still largely unknown in plants, especially in cold sensitive rice. Herein, we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq and MNase-seq) in rice with or without cold treatment. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL18525 GPL23876

31 Samples

Download data: BW, TXT

(Submitter supplied) Cis-regulatory elements (CREs) fine-tune gene transcription during normal growth and development and environmental stress responses in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global genomic sequence and structural variations causative for multi-level changes between Indica and Japonica are still less studied. To answer this question, we here conducted MH-seq (MNase hypersensitive sequencing) for global profiling of open chromatin (MNase hypersensitive sites, MHSs) between two typical Oryza sativa cultivars, Nipponbare (NIP) and 93-11. more...

Organism:

Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

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

Platforms:

GPL27860 GPL31130

8 Samples

Download data: BED, BW, TXT

(Submitter supplied) GA treatment of wild-type rice and use of DELLA protein mutant for RNA-seq and ChIP-seq. Explaining the chromatin mechanisms of DELLA-mediated gene repression and GA signalling-induced gene activation.

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13834 GPL27860

20 Samples

Download data: BROADPEAK, BW, CSV

(Submitter supplied) The Fe(II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. In this work we found that loss-of-function of the rice ALKBH1 gene led to increased 6mA in R-loop regions of the genome but had a limited effect on the overall 6mA level. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL18525

24 Samples

Download data: BROADPEAK, BW, NARROWPEAK, TXT