GEO DataSets

(Submitter supplied) Innovative strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. Traditionally, in Southern-East Asian countries, rice farming benefits from the use of Azolla spp., either as green manure or as co-cultivated plants, for the supply of nitrogen. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: XLSX

(Submitter supplied) Background Rice farming faces a serious challenge from the brown planthopper (BPH), with the pyramiding of BPH14 and BPH15 genes delivering effective protection in elite rice strains. However, the molecular basis behind this resistance is still unclear. Results The study investigated miRNA levels in BPH14/BPH15 pyramiding line (B1415) and their recurrent parent (RP) under BPH infestation employing high-throughput sequencing and revealed 136 differentially expressed miRNAs (DEMs) among 550 known miRNAs. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

18 Samples

Download data: TXT

(Submitter supplied) Jasmonate is an essential phytohormone involved in plant development and stress responses. Jasmonate perception occurs through the COI nuclear receptor allowing to target the JAZs repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of JA-responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

18 Samples

Download data: TXT

(Submitter supplied) To investigate the molecular mechanisms about how OsMP1 regulates rice blast resistance, we established the CR4 line in which target gene has been knocked down by CRISPR-Cas9 gene editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of CR4 and wild-type Hei.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: TXT

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:

Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

18 Samples

Download data: TXT

(Submitter supplied) INO80, one member of ATP-ase remodeler factor, play a role on chromatin dynamic modulation. OsINO80 (LOC_Os03g22900) is identified as a homologue of INO80 in rice. To study the function of OsINO80 on H2A.Z, we analyzed the distribution of OsINO80 and H2A.Z in 14-week-old seedling of Oryza stative Japanese rice plant through ChIP assay following by high through sequencing (ChIP-seq).Integrated analysis showed that OsINO80 regulate the H2A.Z level.

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: BIGWIG

(Submitter supplied) Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation. Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: CSV

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27660

2 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: BIGWIG

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27660

4 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Other

Platform:

GPL27660

2 Samples

Download data: FA

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19290 GPL27660

6 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL27660

14 Samples

Download data: BIGWIG, FA, TXT

(Submitter supplied) We identified the nup1 mutant rice that exhibited specific male sterility due to the absence of Ubisch body formation and pollen grain production. We cloned the causal gene and demonstrated that NUP1, a class III peroxidase predominantly expressed in the anther wall, mediated ROS scavenging. The loss-of-function of NUP1 resulted in ROS burst in anthers, which disrupted the oxidation-reduction process and carbohydrate and lipid metabolisms, and thereby led to loss of tapetal Ubisch bodies and ultimately resulted in male sterility in rice. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19290 GPL27660

60 Samples

Download data: TXT

(Submitter supplied) We identified the involvement of OsPSKR in perceiving PSK as KO plants were almost insensitive to PSK treatment

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

16 Samples

Download data: TXT

(Submitter supplied) The rice Zaxinone Synthase (ZAS) gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone in vitro. Here, we generated and characterized constitutive ZAS-overexpressing rice lines, to better understand ZAS role in determining zaxinone content and regulating growth and architecture. ZAS overexpression enhanced endogenous zaxinone level, promoted root growth and increased the number of productive tillers, leading to about 30% higher grain yield per plant. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: TXT

(Submitter supplied) Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and -enriched proteins that are linked to the functional specificity of individual tissues. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL27660

96 Samples

Download data: BW, CSV

(Submitter supplied) Current methods for R-loop profiling need to perform experiments for each sample individually, with consequent limitations in throughput. Here, based on the barcoding strategy, we develop mDRIP-seq, a high-throughput method showing equivalent performance as conventional methods, but with merits of 7-fold less cost and 6-fold less hand-on time per sample. We also show the simplicity and effectiveness of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Mus musculus; Escherichia coli; Arabidopsis thaliana; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

6 related Platforms

384 Samples

Download data: BW, TXT