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.

2016-07-20 | PXD004603 | JPOST Repository

Transcriptome analysis of rice infected with Rice black streak dwarf virus

2012-12-01 | GSE34263 | GEO

Transcriptome analysis of rice infected with Rice black streak dwarf virus

Project description:Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection. Comparison between RBSDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

2012-12-01 | E-GEOD-34263 | biostudies-arrayexpress

Alterations of rice (Oryza sativa L.) DNA methylation patterns associated with gene expression in response to Rice black-streaked dwarf virus

Project description:High-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified at CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. And meanwhile, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 71 genes with negative relationship between methylation level at promoter regions and gene expression. Many of them were significantly enriched in the KEGG pathways of biosynthesis of amino acids, plant-pathogen interaction and plant hormone signal transduction.

2020-10-28 | GSE150378 | GEO

Oryza Sativa and Magnaporthe Grisea LongSAGE

Project description:LongSAGE library in this series are from 'Whole Genome Analysis of Pathogen-Host Recognition and Subsequent Responses in the Rice Blast Patho-System' project. This work is supported by NSF-PGRP #0115642. Keywords: other

2004-11-08 | GSE1924 | GEO

Characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

Project description:Whole-genome DNA cytosine methylation profiling was used to characterize a knock-down RNA interference line of rice OsNRPD1

2019-08-12 | GSE135738 | GEO

Oryza sativa cultivar:Nippobare Transcriptome or Gene expression

Project description:We used RNA-Seq to systematically investigate the global transcriptomes of rice which was inoculated with viruliferous SBPH, or inoculated with insect-derived RSV or plant-derived RSV by mechanical inoculation, and generated a useful resource for the immune reaction of rice in face of different kinds of RSV. The changes in the expression of candidate transcripts may provide valuable information for future studies on molecular mechanisms of rice stripe disease.

2015-10-18 | E-MTAB-5025 | biostudies-arrayexpress

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