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Phaeodactylum tricornutum

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

PROVIDER: PRJNA279965 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1947730.fastq.gz	Fastqsanger.gz
	SRR1947731.fastq.gz	Fastqsanger.gz
	SRR1947732.fastq.gz	Fastqsanger.gz
	SRR1947723.fastq.gz	Fastqsanger.gz
	SRR1947733.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

2016-03-31 | GSE67449 | GEO

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

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.

2016-03-31 | E-GEOD-67449 | biostudies-arrayexpress

Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

Project description:Chromatin organization in Phaeodactylum tricornutum

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Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

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Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

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Project description:Phaeodactylum tricornutum transcriptome

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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

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Project description:Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum.

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Project description:Phaeodactylum tricornutum Genome sequencing

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