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.
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.
Project description:We analyzed the transcriptomic profile of EFR:XA21:GFP rice lines treated with elf18 to identify genes differentially regulated during this response. We sequenced cDNA from EFR:XA21:GFP leaves treated with 500 nM elf18 for 0.5, 1, 3, 6, and 12 h. We also included untreated EFR:XA21:GFP and Kitaake as controls. Note: All samples in SRA were assigned the same sample accession (SRS843490). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
Project description:In this study, we examined the transcriptome dynamics within the matured fully expanded rice leaf and used strand-specific RNA sequencing to generate a comprehensive transcriptome dataset for the mature rice leaf. The rice Nipponbare (Oryza sativa l. japonica) seedlings were grown in the greenhouse. About 20 days after planting, the fully opened 4th leaves was cut it into seven 3-cm segments, from bottom to tip and labeled as sections 1 to 7, respectively. The tissues were immediately frozen in liquid nitrogen for total RNA extraction. Two biological replicates were collected for each section. Note: All samples in SRA were assigned the same sample accession (SRS685294). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
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.