Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA109973 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nucleosome free measurement of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery 5 conditions: control (30C, liquid media; at 0.5h, 2h, 4h); Heat (transferred from 30C to 40C; at 0.5h, 2h, 4h); Heat recovery (transferred back to 30C after 2h at 40C; after 2h); Dehydration (roots exposed to air; at 2h); Dehydration recovery (roots returned to liquid media after 1.5h in air; after 2h) Samples: 2 biological replicates.
2016-07-03 | E-GEOD-75794 | biostudies-arrayexpress
Project description:Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-changeââ¥â2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down).
2015-08-30 | E-MTAB-4195 | biostudies-arrayexpress
Project description:RNA-dependent RNA polymerase 6 (RDR6) is a core component of the small RNA biogenesis pathway, but its function in meiosis is unclear. Herein we report a new allele of OsRDR6 (Osrdr6-mei), which causes meiosis-specific phenotype in rice. In Osrdr6-mei, meiotic DSB formation was blocked to some extent. We further created a biallelic mutant, Osrdr6-bi, by crossing Osrdr6-mei with a knock out mutant, Osrdr6-edit (Osrdr6-edi). In Osrdr6-bi, 24 univalents were observed at diakinesis, and no histone H2AX phosphorylation (γH2AX) foci was detected in meiocytes, indicating that OsRDR6 is crucial for meiotic DSB formation. Compared with the wild type, the number of 21-nt small RNAs was dramatically reduced, while the number of 24-nt small RNAs was significantly increased in Osrdr6-mei. And thousands of DMRs discovered in Osrdr6-mei, implying that OsRDR6 plays an essential role on DNA methylation, especially CHH methylation. Meanwhile, the transcriptome data showed that 457 genes were down-regulated in the mutant; including three genes related to DSB formation: OsSDS, P31comet and CRC1. Interestingly, the increased 24-nt small RNA level surrounding down-regulated genes was largely associated with the silencing of these genes, while DMRs were rarely related to them. In summary, we speculated that the small RNA levels are disordered in Osrdr6 mutants, which may lead to the defection of DSB formation.
2021-06-05 | GSE151871 | GEO
Project description:This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis. 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control) and 50 ppm Si (1.78 mM) and potassium in the control treatment was balanced with K2SO4 supply. The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1). Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer. To examine transcription of genes related to suberin and lignin synthesis, a self developed microarray containing amongst others ABC transporter, aclytransferases, ß-ketoacyl-CoA synthases and peroxidases was used .
2010-10-10 | GSE23723 | GEO
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:In this study, we used RNA-Seq to understand the mechanisms of Cd toxicity, cellular detoxification and protection pathways in response to Cd in rice roots. To gain additional insight into the rice transcriptomic response to environmental Cd stress, 15-day-old rice seedlings were treated with 10 or 100 μM solutions of Cd2+, or without Cd (control), for 24 h, at which point root samples were harvested and labeled as Cd+, Cd++, and control, respectively. These samples were used for 101 bp paired-end (PE) deep sequencing on an Illumina HiSeq 2500 platform.
2015-06-08 | E-MTAB-4445 | biostudies-arrayexpress
Project description:Proteomics analyses of roots and shoots of O. sativa plants exposed to cold stress.
2022-02-16 | PXD028712 | Pride
Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
2009-06-08 | GSE16248 | GEO
Project description:Here, we first reported the construction of a phosphoproteomic landscape of 6 tissues, including callus, leaves, roots, shoot meristem (SM), young panicles (YP) and mature panicles (MP), from Nipponbare (Oryza sativa ssp. japonica). By employing a non-gel, quantitative phosphoproteomic approach, a total of 4792 phosphopeptides from 2657 phosphoproteins were identified, which were found to be differentially phosphorylated among tissues.
2018-04-11 | PXD005241 | Pride
Project description:In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5’ and 3’ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.
2012-07-27 | GSE39695 | GEO