2024-09-09
ENA first public
ERC000011
ENA-CHECKLIST
Department of Biological Sciences University of Bergen, Bergen, Norway
INSDC center name
public
INSDC status
ERS18586550
SRA accession
E-MTAB-13934:Sample 6
Submitter Id
ArrayExpress
broker name
not collected
collection date
capelin
common name
Protocols: The experiments were performed in August 2019 on the Norwegian Nansen Legacy project cruise to the northern Barents Sea. The fish were collected by trawling in northern Barents Sea and kept in a 500 L tank with running seawater at the ambient seawater temperature outdoor on the deck of the cruise ship in the Northern Barents Sea. Liver slice preparation and culture was using protocols previously described for Atlantic cod (Eide et al., 2014; Yadetie et al., 2018), with a major modification being that the small capelin liver was sliced manually. Liver slice preparation was performed by dissecting the liver, rinsing it in culture medium (Leibowitz-15 medium, Life Technologies™ Gibco®, Paisley, UK) and cutting the entire liver into approximately1 mm cube pieces, using sterile razor blade.  Each well contains slices from a single fish in the complete culture medium (Leibowitz-15 medium supplemented with 10% charcoal-stripped fetal bovine serum and 1% penicillin–streptomycin–amphotericin (10,000 U/mL potassium penicillin, 10,000 μg/mL streptomycin and 25 μg/mL amphotericin B; Sigma-Aldrich)) in the presence of DMSO vehicle control or BaP (0.1, 1, or 10 µM,  at 10°C with horizontal shaking (50 rpm) for 72 hours. Liver slices from a total of 20 fish (biological replicates n = 5 per group). After 72 hours in culture, slices were collected and snap-frozen in liquid nitrogen and stored at -80 °C until further processing. Total RNA was isolated from frozen slices using TRI Reagent according to the manufacturer’s protocol (Sigma-Aldrich, St. Louis, MO, USA). RNA concentration and quality were assessed using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).  Sequenced by Novogene on Illumina NovaSeq 6000 System
description
adult
developmental stage
not collected
geographic location (country and/or sea)
6
individual
not applicable
isolate
Mallotus villosus
organism
Mallotus villosus
organism
liver
organism part
Mallotus villosus
scientific_name
Sample 6
title