{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Fabian Grammes"],"instrument_platform":["NextSeq 1000"],"study_type":["RNA-seq of coding RNA"],"organism":["Salmo salar"],"species":["Salmo salar"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16379"],"description":["In vitro challenge of primary hepatocytes, with the Infectious pancreatic necrosis (IPN) virus. Cells from were infected at MOI 0.1 with two different isolates of IPNV:  V1244 and Vir410/2018. V1244 represents classical IPNV that is affected by the IPN-QTL, while Vir410/2018 is the QTL-insensitive or recent isolate, rIPNV in short."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Liver cells were cultured at 20°C in hepatocyte culture media for a period of two days. After that time, the cells were washed with PBS and fresh culture media was added supplemented additionally with growth factors (5 ng/mL epidermal growth factor (EGF) and 3 ng/mL hepatocyte growth factor (HGF)). At day 7 post-culture, the media was replaced once again to hepatocyte culture media without growth factors.","Sequencing - Sequencing was conducted by NovoGene and BmkGene","Library Construction - Libraries were constructed by NovoGene and BmkGene","Sample Collection - To establish a primary hepatocyte culture, 200 g fish from the Fish Centre facility at NMBU were euthanized by a sharp blow to the head, and the hepatocytes were isolated as previously described: Datsomor, A.K.; Wilberg, R.; Torgersen, J.S.; Sandve, S.R.; Harvey, T.N. Efficient Transfection of Atlantic Salmon Primary Hepatocyte Cells for Functional Assays and Gene Editing. G3 Genes|Genomes|Genetics 2023","Nucleic Acid Extraction - total RNA was extracted using the RNeasy Mini kit (Qiagen®, following the manufacturer’s protocol for extraction from cells. he RNA samples were labelled and stored at -80°C until processed downstream.","Sample Treatment - Two independent challenge tests using primary hepatocytes from 4 different fish (F1 – F4) were performed. Challenge 1 consisted of cells from F1 while the hepatocytes from the remaining fish (F2 – F4) were part of challenge 2. The cells from both challenges were infected in duplicates at MOI 0.1 with cIPNV or rIPNV for 1 hour at 15°C. After incubation time, the viral inoculum was removed and replaced with infection media containing also Amphotericin B (2.5 µg/mL). The cells were kept at 15°C and monitored daily for CPE. Both cells and supernatants were collected for RNA extraction at 4 and 7 dpi for challenge 1 and at 2 and 4 dpi for challenge 2."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Fabian Grammes"],"additional_accession":[]},"is_claimable":false,"name":"IPN in Vitro Challenge","description":"In vitro challenge of primary hepatocytes, with the Infectious pancreatic necrosis (IPN) virus. Cells from were infected at MOI 0.1 with two different isolates of IPNV:  V1244 and Vir410/2018. V1244 represents classical IPNV that is affected by the IPN-QTL, while Vir410/2018 is the QTL-insensitive or recent isolate, rIPNV in short.","dates":{"release":"2025-12-24T00:00:00Z","modification":"2025-12-24T02:01:28.567Z","creation":"2025-12-11T12:58:58.648Z"},"accession":"E-MTAB-16379","cross_references":{"ENA":["ERP186427"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}