title: Transcriptome analysis of long rough dab (Hippoglossoides platessoides) liver slice culture exposed to benzo[a]pyrene.
library_construction_protocol: 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. PCLS preparation was performed by using protocols previously described for Atlantic cod (Eide et al., 2014; Yadetie et al., 2018). The liver was sliced using Leica vibrating blade microtome VT1200 (Leica, Wetzlar, Germany). Slices (300 μm thick strips, about 4 x 4 mm) were cultured in the culture medium (Leibowitz-15 medium, Life Technologies™ Gibco®, Paisley, UK) 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 alone (0.1, 1, or 10 µM,  at 10°C with horizontal shaking (50 rpm) for 72 hours. Liver slices from a total of 5 fish (biological replicates n = 5) were distributed in each group (paired sample design). 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