GEO DataSets

(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 rice miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27908

18 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) Endogenous small RNAs are newly identified players in plant immune responses, yet their roles in rice (Oryza sativa) responding to pathogens are still less understood, especially for pathogens that can cause severe yield losses. Here, we examined the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99, the causal agent of rice bacterial blight disease. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15370

8 Samples

Download data: TXT

(Submitter supplied) African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 Samples

Download data: TXT

(Submitter supplied) Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. more...

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19216

14 Samples

Download data: TXT

(Submitter supplied) To dissect the molecular mechanisms of resistance mediated by Xa39,the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated. A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines’ race 9b.Our results indicated there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: XLSX

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

Organism:

Oryza sativa

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

28 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

24 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from two-week old rice seedlings of jmj704 and wild-type (ZH11) plants to obtain the differntially expressed genes in jmj704 mutant.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

2 Samples

Download data: TXT

(Submitter supplied) An attempt has been made to investigate gene expression patterns of three Xoo strains in XOM2, PXO99 (P6) and PXO86 (P2) from Phillipines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4759 transcripts were identified in this study, and 1151 and 3076 genes were differentially expressed when P6 compared with P2 and P6 compared with C5, respectively. more...

Organism:

Xanthomonas oryzae pv. oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16609

3 Samples

Download data: XLS

(Submitter supplied) RESEARCH SUMMARY Bacterial blight and bacterial leaf streak, two of the most serious diseases of rice, are caused by Xanthomonas oryzae pathovar (pv.) oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) respectively. Xoo is a vascular pathogen that invades the xylem, whereas Xoc is non-vascular and colonizes the mesophyll apoplast. These distinctive types of infection represent the two most common ways plant pathogenic bacteria produce disease. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

60 Samples

Download data: CEL

(Submitter supplied) Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo. Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx. Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13808

16 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

Platforms:

GPL13160 GPL21087

12 Samples

Download data

(Submitter supplied) To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed by RSV infection. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

6 Samples

Download data: TXT

(Submitter supplied) To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed by RSV infection. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21087 GPL13160

6 Samples

Download data: TXT

(Submitter supplied) High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5´and 3´adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. more...

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13925 GPL2025

20 Samples

Download data: CEL, FASTA

(Submitter supplied) An indica rice cultivar IET8585 (Ajaya), resists diverse races of the Xanthomonas oryzae pv oryzae (Xoo) pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. To further understand the mechanism of recessive and durable resistance response, two indica rice genotypes namely, i) IET8585 (Ajaya), a disease resistant indica veriety from India and ii) IR24, a bacterial leaf blight disease susceptible genotype were selected for this study. more...

Organism:

Oryza sativa Japonica Group; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL892

6 Samples

Download data: TXT

(Submitter supplied) We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with  Xanthomonas oryzae pv. oryzae strain PXO99A heterologously expressing the Tal2a effector, the designer TAL effector dT280 which targets a sequence overlapping the predicted Tal2a binding sequence in UCH, or the Tal11b effector. Results provide insight into the genes differentially regulated in a Tal2a- and dT280-specific manner.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 Samples

Download data: TXT