Design: Sea bass were obtained from Station Expérimentale d'Aquaculture Ifremer (Palavas-les-flot, France) with <1g and maintained in Ramalhete Marine Station (CCMAR, Faro, Portugal) in 500 L flow-through seawater tanks, continuously supplied with natural sea water from the lagoon system “Ria Formosa”, at natural temperature and photoperiod and fed with commercial dry pellets. At the day of sampling, six Immature (one year-old) sea bass (18.8 ± 0.3 cm; 75.8 ± 1.1g) were anesthetized in 2-phenoxyethanol (Sigma-Aldrich, diluted 1:5,000 in seawater), washed with clean seawater, measured and weighed. Skin samples (approximately 1 × 0.5 cm) were collected from the pectoral region (Figure 1), which contains a low number of scales, using a scalpel and carefully removing adherent muscle. Individual scales (10/fish) were plucked with forceps from approximately the same position, below the dorsal fin and above the midline, from all fish. Tissues were immediately frozen in liquid nitrogen and stored at -80ºC. Manipulation of animals was performed in compliance with international and national ethics guidelines for animal care and experimentation, under a “Group-I” license from the Portuguese Government Central Veterinary service to CCMAR and conducted by a certified investigator (DMP). Total RNA was extracted from frozen tissues using an automated Maxwell 16 Instrument and a Maxwell 16 SEV total RNA purification kit (Promega, UK) after mechanical disruption using an Ultra Turrax homogenizer (IKA, Germany) using the dispersing element S25N-8G for skin (soft tissue) and S25N-8G-ST for scales (fibrous tissue). Total RNAs of each individual fish were pooled per tissue (0.5µg/fish for skin, 1µg/fish for scales, n=6 fish each tissue) and treated with the DNA-free kit (Ambion, UK) using the optional rigorous treatment, consisting of two sequential 30 min treatments with double the amount of TURBO DNase (4-6 U). RNA concentration and integrity were assessed using an Agilent 2100 Bioanalyser (Agilent Technologies, USA), which confirmed all samples had a RIN (RNA integrity number) above 8. Library preparation was conducted at the Shanghai Ocean University, China using a TruSeq mRNA library prep kit (Illumina, USA), and 0.5ug per library (skin or scale) of RNA. The skin and scale cDNA libraries were subjected to 100 bp paired-end (PE) sequencing using an Illumina HiSeq 1500.
Submitted by: British Antarctic Survey (BAS)
Study:
Dicentrarchus labrax Transcriptome or Gene expressionshow Abstracthide AbstractThe European sea bass (Dicentrarchus labrax) is a marine teleost of great importance in European marine fisheries and aquaculture (FAO 2005) and is also a representative of the species rich order Perciformes that includes many other commercial aquaculture species. Immature (one year-old) sea bass were obtained from a local fish farm (Atlantik fish, Faro, Portugal),
Sample:
Animal sample of Dicentrarchus labraxLibrary:
Name: Dicentrarchus labrax scale
Instrument: Illumina HiSeq 1500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: PCR
Layout: PAIRED
Spot descriptor:
1 forward103 reverse
Runs:
2 runs, 20.1M spots, 4.1G bases, 2.5Gb