GEO DataSets

(Submitter supplied) we compared the change of transcritome between the parents and their F1 hybrids showing different heterosis level and obtained the potential index for predicting the heterosis level between rice parental lines.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

81 Samples

Download data: TXT

(Submitter supplied) To identify direct targets of OsWRKY11 in vivo, we performed chromatin immunoprecipitation sequencing (ChIP-seq).

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

2 Samples

Download data: TXT

(Submitter supplied) We provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

6 Samples

Download data: BW, TXT

(Submitter supplied) In order to investigate the roles of ScOYE3, an old yellow enzyme gene from Saccharomyces cerevisiae, in detoxification and phytoremediation of 2-Nitroaniline (2-NA) in rice, we employed the RNA-seq approach to identify differentially expressed genes in 2-NA-treated wild-type (ZH11) rice plants and transgenic (OE1) rice plants overexpressing ScOYE3. Processing of RNA samples on the Illumina HiSeq 4000 system yielded more than 50 million reads, each 100bp in length, encompassing 6.28Gb of sequence data for each sample which was then mapped to the reference genome. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

8 Samples

Download data: XLS, XLSX

(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) The JA deficient mutant (aoc) showed weaker symptoms than WT when both are exposed to salt. JAs signaling in WT, appeared then to impair salt tolerance and we were interested, through this transcriptomic approach, to highlight the JA-dependent component of the salt stress response that could explain the differential phenotype We report, for root and 2nd leaf, the compared transcriptomes of WT and aoc, before and at 3 different times (1 h, 6 h and 72 h) after salt exposure. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

48 Samples

Download data: CSV

(Submitter supplied) Using acRIP-seq, we present transcriptome-wide atlases of ac4C in Arabidopsis thaliana and Oryza sativa. Analysis of ac4C distribution reveals ac4C is enriched near translation start sites in rice while near translation start sites and end sites in Arabidopsis. Further analysis shows ac4C contributes to RNA stability, splicing and translation. We then performed NaCNBH3 treatment and RNA-seq to measure C to T mutation and RNC-seq to measure translation efficiency in Arabidopsis.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

28 Samples

Download data: BW, XLSX

(Submitter supplied) We explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

6 Samples

Download data: BW, TXT

(Submitter supplied) This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

48 Samples

Download data: XLSX

(Submitter supplied) Purpose: To understand the transcriptional changes during coleoptile senescence, transcriptome libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

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

Platforms:

GPL23013 GPL24468

8 Samples

Download data: TDF

(Submitter supplied) DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well understood in Arabidopsis, mutations in RdDM genes cause no visible developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 in rice. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23013

2 Samples

Download data: TDF, TXT

(Submitter supplied) DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well understood in Arabidopsis, mutations in RdDM genes cause no visible developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 in rice. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23013

2 Samples

Download data: TDF, TXT

(Submitter supplied) Climate change is affecting the unprecedented drought scenario and frequent occurrence of pathogen infection in rice. Simultaneous occurrence of these stresses could lead to more crop loss. Transcription response of genes involved in combined stress would provide relevant candidate gene to develop climate resilient rice. We report individual drought, Xoo infection and combined stress on rice. RNA Seq of contrasting genotypes BPT5204 and TN1 has revealed many candidate genes. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

8 Samples

Download data: CSV, TSV

(Submitter supplied) Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

23 Samples

Download data: CSV

(Submitter supplied) Chilling stress is a major abiotic stress that affects rice growth and development. Rice seedlings are quite sensitive to chilling stress and this harms global rice production. Comprehensive studies of the molecular mechanisms for response to low temperature are of fundamental importance to chilling tolerance improvement. The number of identified cold regulated genes (CORs) in rice is still very small. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23013

12 Samples

Download data: TXT