Oryza sativa Japonica Group
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
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.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Genome diversity analysis of rice varieties from Hokkaido
| PRJDB8749 | ENA
Project description:Analysis of starch properties in glutinous rice cultivars in Hokkaido.
| PRJDB10840 | ENA
Project description:This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells). Keywords: tiling array, genome-wide transcription
2007-02-21 | GSE6996 | GEO
Project description:Genetic studies of early heading in rice in Hokkaido
| PRJDB7712 | ENA
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.
2011-04-07 | GSE28428 | GEO
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.
2015-08-16 | E-MTAB-4372 | biostudies-arrayexpress
Project description:Comparative transcriptome analysis among closely related rice strains
2014-10-27 | E-MTAB-4280 | biostudies-arrayexpress
Project description:In this study, we investigated novel rice genes that are expressed in aleurone cells by RNA-seq. RNA-seq was performed on four samples: a control sample, and samples treated with ABA, GA, and a mixture of the two hormones.
2013-11-14 | E-MTAB-4443 | biostudies-arrayexpress
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