Dataset Information

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

ABSTRACT: Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

PROVIDER: PRJEB48517 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7223150_1.fastq.gz	Fastqsanger.gz
	ERR7223150_2.fastq.gz	Fastqsanger.gz
	ERR7223160_1.fastq.gz	Fastqsanger.gz
	ERR7223160_2.fastq.gz	Fastqsanger.gz
	ERR7223170_1.fastq.gz	Fastqsanger.gz

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Project description:The marine copepod Calanus finmarchicus is the most abundant zooplankton species in the northern regions of the Atlantic Ocean and the Barents Sea. Very little is known about the molecular mechanisms underlying critical processes associated with this species’ complex life history (e.g., ontogenetic development, reproduction, molting, diapause) and physiology (e.g., digestion, neural processes, and membrane physiology). This study analyzed patterns of gene expression of C. finmarchicus samples collected from the Gulf of Maine (Northwest Atlantic Ocean) using a 1,000 expressed sequence tag (EST) microarray designed to assay genes of known physiological function and hypothesized ecological importance for C. finmarchicus. Replicate analyses compared adult females and final-stage juveniles (Copepodite-5) collected from surface (0-30m) and deep (130-170m) layers. Environmental data include detailed characterization of biological, chemical, and physical oceanographic parameters in the sampled water packets. All data were screened for artifacts, normalized and selected using a fold-change filter prior to analysis. Replicate comparisons were analyzed by Significance Analysis of Microarrays (SAM; Stanford University Labs) with a control for False Discovery Rate (FDR) and with Principle Component Analysis with evaluation of significance by one- or two-sample t-test in Acuity Microarray Informatics Software (Molecular Devices, Inc.). Gene Ontology Enrichment Analysis was carried out using GOEAST (http://omicslab.genetics.ac.cn/GOEAST/index.php) to assess functional relationships of selected genes and/or proteins. The results indicated: up-regulation of genes involved in cell division, protein synthesis and mating in deep females and juveniles; up-regulation of genes related to cellular homeostasis, circadian behavior and nervous system development in surface females; and up-regulation of genes related to muscle development and protein catabolism in deep juveniles versus deep females. KEGG pathway analysis using the Blast2GO suite (http://www.blast2go.org/) indicated: up-regulation of genes encoding enzymes related to the citrate cycle and anaerobic metabolism in deep females and juveniles; and up-regulation of genes encoding enzymes related to energy metabolism and osmoregulation in surface females.

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Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

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