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Phaeodactylum tricornutum strain:CCMP2561

ABSTRACT: Phaeodactylum tricornutum transcriptome respionses to shifts in nitrogen source and availability in wild type and nitrate reductase knock out cell lines

PROVIDER: PRJNA311568 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3778923_1.fastq.gz	Fastqsanger.gz
	SRR3778923_2.fastq.gz	Fastqsanger.gz
	SRR3778465_1.fastq.gz	Fastqsanger.gz
	SRR3778465_2.fastq.gz	Fastqsanger.gz
	SRR3776386_1.fastq.gz	Fastqsanger.gz

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

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Project description:Phaeodactylum tricornutum transcriptome respionses to shifts in niitrate availability in wild type and nitrate reductase knock out cell lines (data set 2)

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Project description:The photosynthetic model marine diatom Phaeodactylum tricornutum was cultured with varying nitrogen sources and availability to elicit shifts in the proteome. 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.

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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). 3 biologically independent exponentially growing culture of the WT and the NR21 knock-down were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2.5X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled for 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis after reachign exponential growth.

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Early nutrient starvation response of the diatom Phaeodactylum tricornutum

Project description:An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).

2015-12-07 | E-MTAB-4096 | biostudies-arrayexpress

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

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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

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

2015-01-02 | GSE56346 | 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.

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