GEO DataSets

(Submitter supplied) In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. more...

Organism:

Sorghum bicolor; Oryza sativa

Type:

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

Platforms:

GPL28998 GPL27660

62 Samples

Download data: RDATA

(Submitter supplied) The coordination of pollen viability, stamen filament elongation and anther dehiscence is essential for the successful pollination and reproduction in angiosperms. The hormone jasmonic acid (JA) are crucial for these processes. However, the tight regulation of JA biosynthesis during stamen development is still largely unknown. Here, we demonstrate that the rice (Oryza sativa) ERF-associated amphiphilic repression (EAR) motif-containing protein TCP INTERACTOR CONTAINING EAR MOTIF PROTEIN1 (OsTIE1) tightly regulates JA biosynthesis by repressing TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATINGCELLFACTORS (TCP) transcription factor OsTCP1/PCF5 during stamen development. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33951

11 Samples

Download data: TXT

(Submitter supplied) In order to revael the relationship between gene expression and plant phenotype under drought, we conducted transcriptome analysis under six drought and control conditions.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

576 Samples

Download data: TXT

(Submitter supplied) OsEDS1 is a key regulator of SA-mediated immunity in plants. The OsEDS1 knockout mutant (Oseds1) was characterized and shown to have increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), suggesting the positive role of OsEDS1 in regulating rice disease resistance. To identify differentially regulated downstream of Oseds1, we performed transcriptome deep sequencing (RNA-seq) of wild type (ZH11) and Oseds1 inoculated with Xanthomonas oryzae pv. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: XLS

(Submitter supplied) Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to great yield loss in the context of global climate change. Exploring superior natural variants that confer cold resistance and the underlying molecular mechanism is the major strategy to breed cold tolerant rice varieties. Here, we identified natural variations of a SIMILAR to RCD ONE (SRO) gene OsSRO1c that confers cold tolerance in rice at both seedling and booting stages. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

9 Samples

Download data: TXT

(Submitter supplied) The exocyst is a key factor in vesicle transport and is involved in cell secretion, cell growth, cell division, and other cytological processes in eukaryotes. EXO70 is the key exocyst subunit. We obtained a mutant SHORT-ROOT gene, SR1, through map-based cloning and genetic complementation. SR1 encodes a plant-conserved protein with an EXO70 domain. SR1 mutation affected the whole root-development process, producing shorter radicles, adventitious roots, and lateral roots, abnormal xylem development, causing dwarfing, and decreasing the water potential and moisture content. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: TXT

(Submitter supplied) Twenty-four nucleotide long miRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from MITEs and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. more...

Organism:

Oryza sativa

Type:

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

Platforms:

GPL19290 GPL24468

12 Samples

Download data: BED, BW

(Submitter supplied) The study was conducted to characterize the mutant; identify the candidate gene for the mutant trait with the map-based cloning approach; investigate the segregation of target gene with the mutant characteristics, and examine the metabolic pathways of differentially expressed genes between WT and its mutant with comparative transcriptome analysis.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

6 Samples

Download data: CSV

(Submitter supplied) Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

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

Platforms:

GPL24468 GPL24983

11 Samples

Download data: TDF

(Submitter supplied) To investigate the function of FEM2 in regulation of DNA methylation, 18-day-old seedlings wer used for RNA-seq, BS-seq and sRNA-seq.

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24468

3 Samples

Download data: TDF

(Submitter supplied) To investigate the function of FEM2 in regulation of 24-nt siRNA accumulation, 18-day-old seedlings wer used for RNA-seq, BS-seq and sRNA-seq.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24983

3 Samples

Download data: TDF

(Submitter supplied) To investigate the function of FEM2 in regulation of gene expression, 18-day-old seedlings wer used for RNA-seq, BS-seq and sRNA-seq.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24468

5 Samples

Download data: TDF

(Submitter supplied) During transformation, tissue culture often carries epigenetic and genetic changes underlying somaclonal variations, leading to unpredictable phenotypes. Transformation treatments may individually and jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes have never been examined. Here, we examined the changes in methylomes and transcriptomes associated with each of the components with different combinations of treatments. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL19290

36 Samples

Download data: CGMAP, TXT

(Submitter supplied) To investigate the general effect under normal and low phosphate conditions when MAX1-1400 mutated in rice

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

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; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

10 Samples

Download data: GTF, WIG

(Submitter supplied) Next generation sequencing reveal profiles in H3K27me3 and expression levels between WT and panda mutant, anti-Flag ChIP reveal the binding sites of PANDA protein

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

4 Samples

Download data: GTF

(Submitter supplied) Next generation sequencing reveal profiles in H3K27me3 and expression levels between WT and panda mutant, anti-Flag ChIP reveal the binding sites of PANDA protein

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

6 Samples

Download data: WIG

(Submitter supplied) Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

6 Samples

Download data: TXT

(Submitter supplied) To investigate the role of OsGSE9 in grain shape, we generate its overexpressing lines, and knockout lines by CRISPR/Cas9 system. We then performed gene expression profiling analysis using data obtained from RNA-seq of the panicles of the WT and OsGSE9 transgenic lines

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

9 Samples

Download data: XLSX