Rice root
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA578005 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rice root fungal metagenome Raw sequence reads
| PRJNA810017 | ENA
Project description:root metagenome breed:rice Raw sequence reads
| PRJNA338852 | ENA
Project description:We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones
2024-03-03 | GSE260671 | GEO
Project description:The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. The Phalanx microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 10 independent hybridizations on samples representing two different rice tissues – root and shoot. To examine the gene expression profiles between rice root and shoot development, total RNA extracted from rice root and shoot were processed on the rice OneArray® microarray following the standard protocol using five arrays for each tissue type. Raw expression data from 10 microarrays (e.g. 5 arrays × 2 tissues) were normalized and Pearson’s correlation coefficients were calculated for the data sets of hybridization signal intensities.
2013-09-14 | E-GEOD-50844 | biostudies-arrayexpress
Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar
2018-01-30 | GSE109811 | GEO
Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar
2018-03-03 | GSE111350 | GEO
Project description:Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.
2022-05-02 | GSE180100 | GEO
Project description:black soil-Wild rice controls more root endophytic fungi than cultivated rice Raw sequence reads
| PRJNA667520 | ENA
Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
2020-12-25 | GSE146034 | GEO