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Oryza sativa Japonica Group

ABSTRACT: Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

PROVIDER: PRJNA284956 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2040380.fastq.gz	Fastqsanger.gz
	SRR2040390.fastq.gz	Fastqsanger.gz
	SRR2040400.fastq.gz	Fastqsanger.gz
	SRR2040410.fastq.gz	Fastqsanger.gz
	SRR2040381.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Oryza sativa Japonica Group

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, ebr1 and EIP1-OX Transcriptomes

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Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

Project description: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. Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity. Plants 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). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

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Rice Gene Network Inferred from Expression Profiling of Plants Carrying Xa3/Xa26.

Project description:Japonica rice (Oryza sativa ssp. japonica) variety Mudanjiang 8 (MDJ8) is the wild-type and is susceptible to Xoo. Transgenic rice line Rb49 carries the MR gene Xa3/Xa26, which is driven by its native promoter with the genetic background of MDJ8, and this line is resistant to certain strains (including strain PXO61) of Xoo. Although many studies on Xa3/Xa26-mediated resistace to rice Xoo have been published, the molecular mechanism of this major resistance gene remains poorly understood. Here, we use affymetrix microarray technology to analyze the regulated network mediated by Xa3/Xa26 We used microarrays to study the gene expression network mediated by Xa3/Xa26. Plants 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). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

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Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

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