Oryza
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271253 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1743100_1.fastq.gz | Fastqsanger.gz | |||
| SRR1743100_2.fastq.gz | Fastqsanger.gz | |||
| SRR1743110_1.fastq.gz | Fastqsanger.gz | |||
| SRR1743110_2.fastq.gz | Fastqsanger.gz | |||
| SRR1743101_1.fastq.gz | Fastqsanger.gz |
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Project description:Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.
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Project description:The histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could eThe histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could enhance gene transcription involved in stress-responsive gene expression. The physiological and molecular mechanisms underlying plant responses to insects are being increasingly studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of transcription of hidden genes in plants damaged by insects remain largely unknown. In current study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-seq). RNA-seq data revealed that 3269 and 4609 genes were up-regulated at 3 h and 12 h after infestation with FAW, respectively. ChIP-Seq analysis revealed 1617 and 2617 genes modified by H3K9ac in rice infested with FAW at 3 h and 12 h, respectively, and H3K9ac was mainly enriched in the transcription start sites of genes.
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