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ABSTRACT: Phaeodactylum tricornutum transcriptome

PROVIDER: PRJNA554372 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR9677670.fastq.gz	Fastqsanger.gz
	SRR9677680.fastq.gz	Fastqsanger.gz
	SRR9677690.fastq.gz	Fastqsanger.gz
	SRR9677700.fastq.gz	Fastqsanger.gz
	SRR9677671.fastq.gz	Fastqsanger.gz

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Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

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Project description:Loss of DNA methylation is traditionally associated with transcriptional up-regulation of transposable elements. Here we describe for the first time expression changes upon loss of DNA methylation in diatoms using Phaeodactylum tricornutum as a model species. The loss of DNA methylation was obtained by generation of DNMT5 KOs, a divergent DNMT with SNF-like domains. Expression analysis confirm the loss of DNA methylation is associated with de-repression of transposable elements in Phaeodactylum tricornutum with indirect effects on protein coding genes.

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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).

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