Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA436599 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6801160_1.fastq.gz | Fastqsanger.gz | |||
| SRR6801160_2.fastq.gz | Fastqsanger.gz | |||
| SRR6801170_1.fastq.gz | Fastqsanger.gz | |||
| SRR6801170_2.fastq.gz | Fastqsanger.gz | |||
| SRR6801180_1.fastq.gz | Fastqsanger.gz |
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Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
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Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
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