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Phaeodactylum tricornutum

ABSTRACT: Time series of native associated bacteria communities under different inorganic nitrogen conditions

PROVIDER: PRJNA803332 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17880910_1.fastq.gz	Fastqsanger.gz
	SRR17880910_2.fastq.gz	Fastqsanger.gz
	SRR17880911.fastq.gz	Fastqsanger.gz
	SRR17880911_1.fastq.gz	Fastqsanger.gz
	SRR17880911_2.fastq.gz	Fastqsanger.gz

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Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

2015-01-02 | GSE56346 | GEO

Quantitative Analysis of Phaeodactylum tricornutum transcriptomes

Project description:Purpose: Using RNAseq to profile transcriptomes to compare wildtype and PtTryp2 knockout lines across different nutrient conditions, aim to further explore the molecular function of PtTryp2 in regulating cell growth and responses to N- and P-stress. Methods: Libraries for RNAseq were created from 1µg of mRNA from each culture. The resulting libraries were loaded into the patterned nanoarray, and single-end 50 bp reads were generated on BGIseq500 platform (BGI-Shenzhen, China), with a data output of about 22 M total clean reads for each library. Results: Transcriptomic data show that PtTryp2 knockout led to the upregulation of most of the nitrogen assimilation and metabolism genes under both N-depleted and replete conditions. In addition, when comparing N-depleted with N-replete conditions, 646 differentially expressed genes (DEGs) were identified in the blank vector control (KOC) but only 187 in PtTryp2-KO1, considerably fewer in the knockout mutant. Based on RNA-seq, remarkably more DEGs were found for the P-depleted versus nutrient-replete comparison in PtTryp2-KO1 (1501) than that in KOC (277). Besides, in PtTryp2-KO1, the majority of these DEGs (77.25%) exhibited greater fold changes than that in KOC. Conclusions: Transcriptomic data coupling with physiological experiments, suggesting that PtTryp2 knockout led to amplitude magnification of the NO3- and Pi uptake “seesaw”, whereas PtTryp2 overexpression dampened it. All our data demonstrate in concert that PtTryp2 is a coordinate regulator of N-P stoichiometric homeostasis.

2022-06-14 | GSE202896 | GEO

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

2015-01-02 | E-GEOD-56346 | biostudies-arrayexpress

Phaeodactylum tricornutum

Project description:Transcriptome of nitrogen starved and normal cultured Phaeodactylum tricornutum

| PRJNA235975 | ENA

Phaeodactylum tricornutum

Project description:bacteria biodiversity Metagenomic assembly

| PRJNA1120744 | ENA

Phaeodactylum tricornutum

Project description:Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

| PRJNA253958 | ENA

Phaeodactylum tricornutum

Project description:Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

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Next generation sequencing for understading the role of nitrate reductase in remodeling intermediate metabolism in Phaeodactylum tricornutum

Project description:We have done next generation sequencing of optically thin, exponentialy growing WT Phaeodactylum tricornutum and our ~50% nitrate reductase knock-down cultures. Culture were grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation).

2016-03-31 | GSE67449 | GEO

Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

Project description:We combined transcriptional and metabolite analyses to monitor the effect of N deficiency at different molecular levels in order to get better insight on the acclimation strategies P. tricornutum employs under nitrogen limitation. Physiological data like neutral lipid measurement, cell growth and other cell chemistry measurements further complemented our molecular data. We showed that P. tricornutum is able to remobilize nitrogen through catabolism of various internal nitrogen-containing resources such as amino acids and proteins. N starvation was also accompanied by reduction in pigment pools as well as photosynthetic capacity. The global expression data showed that majority of metabolic changes were related to carbon and lipid metabolism. Decreased levels of carbon skeletons due to suppression of the Calvin cycle was compensated by breakdown of chrysolaminaran leading to up-regulation of OPPP, glycolysis, pyruvate metabolism and TCA cycle. These pathways provide precursors for fatty acid biosynthesis. In addition, remodeling of membrane lipids and up-regulation of the de novo TAG biosynthetic pathway was further supported by physiological measurements of neutral lipids, indicating TAG accumulation under N limitation. Our study gives a detailed image of adaptation of P. tricornutum to N starvation, and can be used for future metabolic manipulations to increase TAG production.

2015-06-01 | GSE58946 | GEO

Proteome and phosphoproteome response of the diatom Phaeodactylum tricornutum under varying nitrogen and iron

Project description:The photosynthetic model marine diatom Phaeodactylum tricornutum was cultured under conditions varying nitrogen content and availability, or varying iron concentrations over diel cycles to elicit shifts in the proteome and phosphoproteome. For the nitrogen experiments, cells were grown to mid-exponential phase on ammonium (880 uM), collected by centrifugation and resuspended in N-free media for 2 hrs, and spiked with nitrate (150 uM) for 90 min. Cells were again collected by centrifugation, washed in N-free media, and resuspended in experimental treatments with no nitrogen (N-) and a nitrogen source (300 uM) provided as ammonium, nitrite, or nitrate. Each experimental treatment was sampled after 15 min, 45 min, and 18 hr. For iron experiments, steady-state axenic cultures were maintained under a diel cycle of 12h light: 12h darkness and at three different concentrations of Fe' (Fe' is the sum of all Fe species not complexed to EDTA): a low concentration (20 pM Fe'), intermediate concentration (40 pM Fe') and at Fe-replete levels (400 pM Fe'). Samples were taken every four hours.

2020-04-17 | PXD015059 | Pride

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