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Oryza sativa Japonica Group strain:Nipponbare

ABSTRACT: Rice chromosome 10 alternate assembly

PROVIDER: PRJNA13174 | ENA |

REPOSITORIES: ENA

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Oryza sativa Japonica Group

Project description:rice chromosome 3 alternate assembly

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Project description:rice chromosome 11 and 12 alternate assembly

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Oryza sativa Japonica Group transcriptome sequencing

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

Oryza sativa (japonica cultivar-group)

Project description:Rice alternate assemblies for chromosomes 3, 10, 11, 12

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Oryza sativa Japonica Group strain:Nipponbare

Project description:International Rice Genome Sequencing Project

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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

Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant

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

Classification of rice (Oryza sativa L. Japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress.

Project description: Not available

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Gene expression ATLAS of Oryza sativa sp japonica (cv. Nipponbare) during photomorphogenesis (transition from dark to light)

Project description:Oryza sativa Japonica (rice) is the staple food for all over world population. At the time of germination, the exposure to light may play an important role in the early development of the rice seedling. In order to survey the genes, their functions and role in biological processes, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out to explore transcriptional programs operating in dark and light conditions. For each treatment type, three individual plants were used as biological replicates.

2022-12-01 | E-MTAB-5689 | biostudies-arrayexpress

Oryza sativa japonica Transcriptome or 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.

2015-08-16 | E-MTAB-4372 | biostudies-arrayexpress

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