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Arabidopsis thaliana

ABSTRACT: Genome-wide expression analysis regulated by internal nitrate in the presence of external ammonium in Arabidopsis thaliana

PROVIDER: PRJDB8627 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR186601.fastq.gz	Fastqsanger.gz
	DRR186602.fastq.gz	Fastqsanger.gz
	DRR186603.fastq.gz	Fastqsanger.gz
	DRR186604.fastq.gz	Fastqsanger.gz
	DRR186605.fastq.gz	Fastqsanger.gz

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Arabidopsis thaliana

Project description:Genome-wide expression analysis regulated by internal nitrate in Arabidopsis thaliana

| PRJDB7349 | ENA

Comparison of root transcriptomes in Arabidopsis thaliana plants supplied with different forms of inorganic nitrogen

Project description:Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition. Our goal was to compare the transcriptomes of nitrate-supplied and ammonium-supplied plants, with a particular interest in characterizing the differences in redox metabolism elicited by different forms of inorganic nitrogen. We used microarrays to compare the short-term transcriptional response to either nitrogen supply or ammonium supply in Arabidopsis roots. Genes upregulated or downregulated by nitrate only, ammonium only, or both ammonium and nitrate were identified and analyzed. Arabidopsis thaliana (Col-0) plants were grown hydroponically until they reached growth stage 5.10. They were then transferred to a nitrogen-free medium for 26 hr and then supplied with 1 mM nitrate or 1 mM ammonium. RNA isolation (and subsequent microarray analysis) was performed on root tissue isolated just before nitrogen supply (time 0) and at 1.5 hr and 8 hr after nitrogen supply (1.5 hr nitrate, 8 hr nitrate, 1.5 hr ammonium, 8 hr ammonium).

2011-05-28 | E-GEOD-29589 | biostudies-arrayexpress

Comparison of root transcriptomes in Arabidopsis thaliana plants supplied with different forms of inorganic nitrogen

2011-05-28 | GSE29589 | GEO

Arabidopsis thaliana

Project description:Early transcriptional responses of Arabidopsis thaliana to ammonium and nitrate deprivation

| PRJNA298366 | ENA

Early transcriptional responses of Arabidopsis thaliana to ammonium and nitrate deprivation

Project description:Identification of the earliest transcriptional responses of adult Arabidopsis plant roots towards N-deprivation. Hydroponically grown Plants (35 days old) were 5 days adapted to nitrate or ammonium,respectively, as sole N-source to detect N-form specific transcripts.

2016-05-31 | GSE73903 | GEO

Root and shoot performance of Arabidopsis thaliana exposed to elevated CO2: a physiologic, metabolic and transcriptomic response.

Project description:In this study we explain the physiological, biochemical and gene expression mechanisms adopted by ammonium nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses A transcriptomic analysis enabled the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates in elevated [CO2] conditions.

2017-01-02 | GSE64994 | GEO

Root and shoot performance of Arabidopsis thaliana exposed to elevated CO2: a physiologic, metabolic and transcriptomic response

2017-07-01 | GSE70560 | GEO

Arabidopsis thaliana 25 accessions

Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.

2018-11-14 | ST001096 | MetabolomicsWorkbench

Silver nitrate has a measurebale but minor impact on gene expression in Arabidopsis thaliana

Project description:Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to chronic exposure to silver nitrate at 4 μg/mL concentration. Methods: mRNA was extracted from non-treated and silver nitrate-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were paired-end sequenced (100-nt read length) on an Illumina Nova Seq6000 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 20.0.4, Qiagen). Results: Chronic exposure of A. thaliana plants to silver nitrate caused a change in the abundance of transcripts: AT2G01520 and AT4G12550, but no measureable impact on the rest of the transcriptome. Conclusions: Exposure of A. thaliana to silver nitrate at 4 μg/mL has minor impact on the transcriptome.

2022-03-15 | GSE198360 | GEO

Root nitrate response of wild type plants and afb3-1 mutant plants in Arabidopsis thaliana

Project description:Auxin is a key phytohormone regulating central processes in plants that include embryo development, lateral root growth and flower maturation among others. Auxin is sensed by a set of F-Box proteins of the TIR1/AFB3 family triggering auxin dependent responses by a pathway that involves an interplay between the Aux/IAA transcription repressors and the ARF transcription factors. We have previously shown that the AFB3 auxin receptor has a specific role in coordinating primary and lateral root growth to external and internal nitrate availability (Vidal et al., 2010). In this work, we used an integrated genomics, bioinformatics and molecular genetics approach to dissect regulatory networks acting downstream AFB3 that are activated by a transient nitrate treatment in Arabidopsis roots. Our systems approach unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate. Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 Î¼E/m2/sec) and 8 hours of dark at 22Â°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.

2012-04-30 | E-GEOD-35544 | biostudies-arrayexpress

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