Barley responses to nitrate limitation-BarIEy Stress Tolerance
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ABSTRACT:
ORGANISM(S): Hordeum vulgare
PROVIDER: GSE188216 | GEO | 2022/01/24
REPOSITORIES: GEO
Similar Datasets
Project description:barley responses to nitrate limitation-BarIEy Stress Tolerance
| PRJNA777933 | ENA
Project description:Diatom transcriptomics under nitrate limitation
| PRJNA242525 | ENA
Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling.
2014-03-25 | GSE56132 | GEO
Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 M-NM-<M NaNO3, 212 M-NM-<M Na2SiO3, 72.4 M-NM-<M NaH2PO4) or during mid-exponential growth in nutrient-replete media (882 M-NM-<M NaNO3, 106 M-NM-<M Na2SiO3, 36.2 M-NM-<M NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=18). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for the nitrate-limited treatment were normalized to pooled counts for the nutrient-replete M-bM-^@M-^\controlM-bM-^@M-^] treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.
2014-03-25 | E-GEOD-56132 | biostudies-arrayexpress
Project description:We performed a comparative phosphoproteomic analysis of Arabidopsis root membrane proteins of WT and nrt1.1-1 under low nitrate (LN) and high nitrate (HN) availability in order to identify the downstream components that may be involved in NRT1.1-dependent LR growth and signal transduction.
2024-02-22 | PXD048853 | Pride
Project description:Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.
2016-12-01 | GSE71880 | GEO
Project description:To identify the differetially expressed genes under nitrate stress, RNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were mapped to rice (IRGSP-1) genome.
2022-04-01 | GSE166667 | GEO
Project description:Freshly harvested Arabidopsis seeds (ecotype Col0 obtained under 10 mM nitrate nutrition, referred to as C10) are dormant and do not germinate when sown on an agarose-based medium. This experiment was performed to analyze the genes that are differentially expressed in freshly harvested C10 seeds sown on agarose (dormant) versus freshly harvested C10 dry seeds (dormant) to analyze differential expression of genes during the first 6 hrs of imbibition of dormant seeds. Reference: Alboresi et al. Plant Cell Environ (2005) 28 : 500-512 - 16 DAP siliques were harvested from Col 0 plants grown on 10 or 50 mM nitrate or from G4 3 mutant grown on 10 mM nitrate in growth chambers. Keywords: treated vs untreated comparison
2007-05-31 | GSE7934 | GEO
Project description:To identify the differetially expressed sRNAs under nitrate stress, sRNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were processed and analysed using UEA sRNA workbench.
2022-04-01 | GSE166668 | GEO
Project description:ra05-12_nar2 - atnar2.1-1 - Does the ko of AtNAR2.1 leads to a differential expression in comparison to the WT when grown under high nitrate condition and transfered onto low nitrate concentration? - Plants were grown for 41 days in hydroponics in media containing 6 mM nitrate and then transferred to 6 or 0.2 mM nitrate media for 24h ( short days, irradiation 150 uE). Plants were harvested on day 42 during the first 2 hours of light. Keywords: dose response,gene knock out
2008-03-12 | GSE10705 | GEO