Project description:This study aims to provide a transcriptomics dataset for field grown rice plants subjected to mild drought concentrating on the two parents of a mapping population, Bala and Azucena. Plants were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007. Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. The drought was imposed for 24 days during which time a small amount of water was added on 3 occasions to raise soil moisture to 30% by volume. After 24 days the second youngest fully expanded leaf was taken and gene expression analysis performed. We used microarrays to detail the global programme of gene expression underlying drought in rice plants with the aim of using the data to identify candidate genes for drought avoidance QTLs detected within the a rice mapping population.
Project description:This transcriptome experiment identified a core set of genes differentially regulated under submergence between tolerant and sensitive rice genotypes. This differential modulation of gene expressions could contribute to the level of flooding tolerance in diverse rice genotypes. Rare allele-specific gene regulations and genotype-specific adaptive mechanisms could further promote the submergence tolerance in those genotypes with extremely adaptive phenotype.
Project description:<p>Pigmented rice (<em>Oryza sativa L.</em>) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.</p>
Project description:we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types . We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms.
Project description:Corresponding data set is composed of RNA sequencing of Korean ER positive breast cancer under 35 years old. This set provides 50 alignment files of 50 tumor samples. This is a part of total project data set.
| EGAD00001003243 | EGA
Project description:Resequencing data of 120 rice RILs
| PRJNA522923 | ENA
Project description:Resequencing data of 147 rice varieties
