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RNA-seq transcriptome profiling of the Southern Ocean diatom Fragilariopsis cylindrus under different experimental conditions, silica limitation and two different light spectra

ABSTRACT: RNA-seq transcriptome profiling of the Southern Ocean diatom Fragilariopsis cylindrus under different experimental conditions, silica limitation and two different light spectra

PROVIDER: PRJEB19093 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR1802040_1.fastq.gz	Fastqsanger.gz
	ERR1802040_2.fastq.gz	Fastqsanger.gz
	ERR1802031_1.fastq.gz	Fastqsanger.gz
	ERR1802031_2.fastq.gz	Fastqsanger.gz

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RNA-seq transcriptome profiling of the Southern Ocean diatom Fragilariopsis cylindrus under different experimental conditions, silica limitation and two different light spectra

Project description:The Southern Ocean diatom Fragilariopsis cylindrus was grown under half-saturating concentrations of silicate (0.3 uM) and in the blue (480 - 540 nm) and red (550 - 700 nm) light spectrum to investigate gene expression responses using RNA-seq relative to optimal growth conditions (deposited under accession E-MTAB-5024). RNA-seq was performed on three replicate samples for each experimental condition. Total RNA was extracted using a guanidinium thiocyanate-phenol-chloroform extraction protocol, followed by DNase I treatment and RNA purification (Quiagen). First strand cDNA synthesis was performed using random hexamers. Library preparation was performed using the RNA-seq Sample Prep Kit (Illumina) and sequencing was conducted according to the TruSeq RNA sequencing protocol (Illumina) All samples were sequenced together in one flowcell on one lane.

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Project description:We performed RNA-sequencing experiments to examine the differential regulation of genes in the genome of the Southern Ocean diatom Fragilariopsis cylindrus including diverged alleles. RNA-seq was performed on three replicate samples for each experimental condition. Phytoplankton cells were grown under six different experimental conditions including (1) optimal growth, (2) freezing temperatures, (3) elevated temperature, (4) elevated carbon dioxide concentrations, (5) low iron concentrations and (6) prolonged darkness. Total RNA was extracted using a guanidinium thiocyanate-phenol-chloroform extraction protocol, followed by DNase I treatment and RNA purification (Quiagen). First strand cDNA synthesis was performed using random hexamers. Library preparation was performed using the RNA-seq Sample Prep Kit (Illumina) and sequencing was conducted according to the TruSeq RNA sequencing protocol (Illumina) All samples were sequenced together in one flowcell on one lane.

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