Ontology highlight
ABSTRACT:
PROVIDER: PRJNA792427 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17399976_1.fastq.gz | Fastqsanger.gz | |||
| SRR17399976_2.fastq.gz | Fastqsanger.gz | |||
| SRR17399977_1.fastq.gz | Fastqsanger.gz | |||
| SRR17399977_2.fastq.gz | Fastqsanger.gz | |||
| SRR17399978_1.fastq.gz | Fastqsanger.gz |
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Project description:In comparison with provision of either ammonium or nitrate alone, simultaneously supplying both forms of N results in superior growth and yield for the majority of plants including rice. Using a rice 22K oligo-array, we performed transcriptome analysis to identify genes of rice (Oryza sativa L. ssp. japonica) responsive to change of N-supply forms and N-starvation. Using the supply of ammonium nitrate (one to one molar ratio) as control, the total number of root genes that were equal or more than two fold up- or down- regulated was 445, 324, and 781 by upon supply of either ammonium or nitrate or continuous N starvation, respectively for 96 h. In the shoot the equivalent numbers were much smaller only 32, 58, and 165, respectively. Clustering of the rice genes associated with different environmental stresses revealed substantial organ specificity of the root and shoot to N starvation, and also to the N supply form. Genes encoding transporters for ammonium and nitrate, nitrate reductase, glutamate dehydrogenase, and aspartate amino transferase, showed great response to change of the N supply form, especially to N starvation. Some of the genes involved in chlorophyll metabolism, carbon fixation and assimilation, were enhanced by ammonium supply only, but significantly suppressed by N-starvation. In the shoot there was increased expression of more general stress genes under nitrate when compared to ammonium nutrition. In the root the reverse situation was true with more apparent stress under ammonium nutrition. The microarray approach has revealed new levels of complexity in the response of rice to the form of N supply. Keywords: Rice; root; shoot; nitrogen starvation; nitrogen form; ammonium; nitrate; gene expression
2006-12-07 | GSE4409 | GEO
Project description:A tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for the peptidomic analysis.
2023-03-11 | PXD037574 | Pride
Project description:OsNRAMP5 is involved in iron, manganese and cadmium transport. Goal was to determine the effects of knocking down OsNRAMP5 on global rice gene expression. Two experiments: Control condition experiment: root or shoot of WT vs. OsNRAMP5 RNAi plants. WT Cd treatment experiment: 4 weeks old WT plants grown under 0 or 10uM Cd for two weeks
2012-02-03 | E-GEOD-35502 | biostudies-arrayexpress
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:transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv M-bM-^@M-^XI Kong PaoM-bM-^@M-^Y ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures. 8 samples, Two-condition experiment, control (0 ppm ferrous iron) vs. iron treated (125 ppm ferrous iron). Biological replicates: 2 replicates for comparison shoot 3 days of stress, root 3 days of stress, shoot 3 weeks of stress and root 3 weeks of stress.
2012-05-14 | E-GEOD-36299 | biostudies-arrayexpress
Project description:In comparison with provision of either ammonium or nitrate alone, simultaneously supplying both forms of N results in superior growth and yield for the majority of plants including rice. Using a rice 22K oligo-array, we performed transcriptome analysis to identify genes of rice (Oryza sativa L. ssp. japonica) responsive to change of N-supply forms and N-starvation. Using the supply of ammonium nitrate (one to one molar ratio) as control, the total number of root genes that were equal or more than two fold up- or down- regulated was 445, 324, and 781 by upon supply of either ammonium or nitrate or continuous N starvation, respectively for 96 h. In the shoot the equivalent numbers were much smaller only 32, 58, and 165, respectively. Clustering of the rice genes associated with different environmental stresses revealed substantial organ specificity of the root and shoot to N starvation, and also to the N supply form. Genes encoding transporters for ammonium and nitrate, nitrate reductase, glutamate dehydrogenase, and aspartate amino transferase, showed great response to change of the N supply form, especially to N starvation. Some of the genes involved in chlorophyll metabolism, carbon fixation and assimilation, were enhanced by ammonium supply only, but significantly suppressed by N-starvation. In the shoot there was increased expression of more general stress genes under nitrate when compared to ammonium nutrition. In the root the reverse situation was true with more apparent stress under ammonium nutrition. The microarray approach has revealed new levels of complexity in the response of rice to the form of N supply. Experiment Overall Design: Rice seedlings were grown in a hydroponic system in a growth chamber with control of both temperature and light. After normal growth for two weeks and for one week with completely avoiding any N source, the plants at four and a half leaf stage were re-supplied with ammonium nitrate (equal amount of either form of N), or only ammonium (ammonium sulphate and ammonium chloride), or only nitrate (calcium nitrate and magnesium nitrate), and continuing at zero N (N starvation). All the other essential nutrients were the same for all four treatments, except for sulfate and chloride which ranged between 1.1 â 2.6 mM and 0.5 â 2.5 mM, respectively. In Arabidopsis, addition of 3 mM Cl to âcontrolsâ did not produce any changes in the expression of genes in an experiment investigating the re-supply of 3 mM nitrate (Scheible et al., 2004). In other microarray experiments, extra addition of 5 mM Cl for Arabidopsis (Wang et al., 2000; Wang et al., 2004) and 1.4 mM sulphate for tomato (Wang et al., 2001) were used to replace nitrate for identifying the N deprivation responsive genes. Therefore, we assume that the relative smaller difference in sulfate and chloride concentrations among the four treatments in the normal supply range for plants would not significantly affect the expression profile of genes responsible for changes in N supply form and starvation in our experiments. Experiment Overall Design: For identifying the genes responding to the various N conditions by micro-array analysis, we extracted total RNA respectively from the roots and shoots at the 96 h after initiation of the four respective treatments. We used amplified and labeled cRNA from ammonium nitrate treatment as control, we performed array-hybridization for the cRNA from the treatment of single ammonium form, single nitrate form, or continuous N depletion, respectively. Agilent 60-mer oligonucleotide arrays containing 21,938 unique transcription units (Agilent Technologies, Tokyo, Japan) were used. Two biological replicates of each treatment were performed for microarray analyses.
2008-06-13 | E-GEOD-4409 | biostudies-arrayexpress
Project description:This study aims to deal with a comparative proteome analysis of shoot and root tissues of contrasting phosphorus (P) responsive rice genotypes (Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL). Proteins were isolated from shoot and root tissues collected from 45-day-old rice plants grown hydroponically in PusaRicH medium with P (16ppm, +P) or without P (0 ppm, -P) under controlled environmental conditions. Following protein quantification using the Bradford method, and quality check using 1D SDS-PAGE, trypsin was used for in-solution digestion and Nano ACQUITY UPLC-MS/MS was used to separate and identify peptides. This study aimed at deciphering the molecular aspect of Pup1 QTL in P-starvation stress tolerance in rice.
2023-02-27 | PXD039084 | Pride
Project description:Here we report the genome-wide transcriptomic changes resulting from low N stress, low water (W) stress and both the stresses (N-W-) from root and shoot tissues in two rice genotypes,IR 64 (IR64) and Nagina 22 (N22).The former is a better N user but drought stress sensitive while the latter is the internationally known drought tolerant variety but with poor NUE. Though it is well known that adverse effect of the major abiotic stress, drought, on rice is exacerbated by low supply of N, there are no studies yet on the genome-wide effect of co-occurrence of these two major inputs, water and N. We identified a total of 8926 unique differentially expressed genes (DEGs) across all stress treatments compared to optimal input supply. Interestingly, we identified only 1174, 698 and 903 DEGs in root tissues of IR 64, and 1197, 187 and 781 DEGs in N22; while nearly double the number of DEGs were found in shoot tissues, i.e., 3357, 1006 and 4005 in IR 64 and 4004, 990 and 2143 DEGs (log 2 fold change and FDR p value <0.05) in N22 under N-W+, N+W- and N-W-stress treatments.Overall, more than 70% of the genes showed a similar response in both the genotypes. Of the 15 differentially expressed N transporter genes including the high affinity nitrate transporters, ammonium transporters and urea transporter, IR64 showed differential expression in all of them whereas N22 showed differential expression only in 11 under N-W-and/or N-W- stress(es). Four of the N transporters (NRT2.1, NRT2.4, OsNAR2.2 and OsAMT2_1) were also differentially expressed under N+W-condition. A low affinity nitrate transporter, OsNPF7.2, was differentially expressed only in N22 shoots under all three stress conditions implicating its genotype specific role in nitrate transport in above ground part. Genes involved in allantoin and melatonin metabolism were down regulated only under N stress in both the genotypes but not under drought. Three negative regulators of N stress, NIGT1, OsBT and OsACTPK1 were downregulated in IR64 while NIGT1 transcript alone was downregulated in N22 under N stress. Of the 8926 DEGs, 26.15% were completely novel represented by 916 conserved hypothetical proteins and 1418 hypothetical conserved_gene/gene/proteins.
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Project description:RNA-seq was performed on shoot and root from 42 day-old plants of nlps mutants and WT grown on sand under non-limiting nitrate supply (5mM).
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