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E-MTAB-6983

ABSTRACT: RNA sequencing of Oryza sativa ssp. indica of inbred and derived epilines

PROVIDER: E-MTAB-6983 | ExpressionAtlas | 2019-01-16

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-6983-analysis-methods.tsv	Tabular
	E-MTAB-6983-analytics.tsv	Tabular
	E-MTAB-6983-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-6983-configuration.xml	Xml
	E-MTAB-6983-g4_g1-mvaPlot.png	Other

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Project description:The contained data consist of Illumina HiSeq reads generated genomic RNA of Oryza sativa ssp. indica used for RNA-seq analysis. The inbred control line and derived epilines LR1, LR2 and LR3 of the 4th selfing were analysed using RNA-seq.

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Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for WGBS analysis. The inbred control line and derived epilines LR1, LR2 and LR3 of the 4th selfing were analysed using whole-genome bisulfite sequencing. Control and LR2 lines can be found in ArrayExpress E-MTAB-5002 submission, LR1 and LR3 are part of this submission

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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

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Dynamic Profiles of transcriptome in Oryza sativa leaf

Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

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