GEO DataSets

(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) 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) 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:

GPL27960 GPL21027 GPL18525

9 Samples

Download data: TXT

(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:

GPL23876 GPL18525

31 Samples

Download data: BW, TXT

(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

(Submitter supplied) To investigate whether observed changes in pre-mRNA splicing led to OsFKBP20-1b depletion, we analyzed RNA-seq to identify the quantitative profiling and alternative splicing

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

12 Samples

Download data: XLSX

(Submitter supplied) To reveal the involvement of OsERF096 in response to cold stress, this study performed transcriptome sequencing of WT, OsERF096-OX and OsERF096-RNAi rice before and after cold stress.Based on transcriptome sequencing, this study found that OsERF096 is involved in the regulation of hormone signal transduction.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

18 Samples

Download data: TXT

(Submitter supplied) In our study, we identified a new transgenerational epigenetic mutant in rice, Epi-LF (Epi-LongFeng). The metastable phenotype of Epi-lf resembles that of rice Epi-d1, and the inheritance is largely similar to that of the agoutiAy mouse mutant. We found that in Epi-lf,mCHH methylation was present in a 155-bp sequence of DNA in close proximity to the 3' end of the LF gene, but the abundance of the siRNAs corresponding to this region was not significantly different from that of the wild type (WT), suggesting that this is a mCHH island like modification. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL21812 GPL23876 GPL18525

63 Samples

Download data: CSV, TXT

(Submitter supplied) Popular rice mega varieties lack sufficient key micronutrients (e.g., Fe, Zn), vitamins and a balanced amino acid composition that are essential for a healthy diet. The major bottleneck for improving the nutritional quality of popular rice varieties through conventional breeding or gene technology is our lack of an integrated understanding of the biochemical and molecular processes that occur during rice grain filling (and their determining genes or loci). more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

28 Samples

Download data: XLSX

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL27908 GPL18525

20 Samples

Download data: TXT

(Submitter supplied) we emphatically monitored the responsive changes of genes targeted by rice miRNAs miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by degradome technology.These findings provide new insights into the complex roles of characteristic miRNAs in rice-Xoo interactions.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

2 Samples

Download data: TXT

(Submitter supplied) In rice, tillering is an important agricultural trait that affects plant architecture and grain yield. RNA-directed DNA methylation (RdDM), which establishes DNA methylation in all CG, CHG and CHH sequence contexts and maintains CHH methylation in plants, silences transposable elements (TEs) and regulates gene expression. Here we report that knockdown and knockout of OsNRPD1a and OsNRPD1b, genes encoding two orthologues of the largest subunit of OsPol IV holoenzyme that transcribes 24-nucleotide (nt) siRNAs in RdDM, lead to a high-tillering phenotype, in addition to dwarfism and smaller panicles. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL18525 GPL23876

18 Samples

Download data: BW, TXT

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

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

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

Platforms:

GPL23013 GPL18525

36 Samples

Download data

(Submitter supplied) Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18525

18 Samples

Download data: XLSX

(Submitter supplied) The genome-wide gene expression differences between the control (ZH17) and OEZ after cold treatment.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

6 Samples

Download data: TXT

(Submitter supplied) Two types of small (18-24 nt) non-coding RNAs (ncRNAs), microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been found to exist widely in higher plants. OsDCL3b has just been reported to process the 24-nt phased small RNAs in rice, which are preferentially expressed in panicle. In this study, we find that down-regulated expression of OsDCL3b leads to lower pollen sterility and seed setting rate, which results in decreased grain yield per plant in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL18525

8 Samples

Download data: XLS

(Submitter supplied) Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

6 Samples

Download data: XLSX

(Submitter supplied) Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

21 Samples

Download data: TXT